ClinVar Genomic variation as it relates to human health
NM_144773.4(PROKR2):c.254G>A (p.Arg85His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Pathogenic(4); Likely pathogenic(6); Uncertain significance(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_144773.4(PROKR2):c.254G>A (p.Arg85His)
Variation ID: 3451 Accession: VCV000003451.46
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 20p12.3 20: 5314116 (GRCh38) [ NCBI UCSC ] 20: 5294762 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jul 2, 2015 Apr 15, 2024 Mar 26, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_144773.4:c.254G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_658986.1:p.Arg85His missense NC_000020.11:g.5314116C>T NC_000020.10:g.5294762C>T NG_008132.2:g.5254G>A Q8NFJ6:p.Arg85His - Protein change
- R85H
- Other names
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- Canonical SPDI
- NC_000020.11:5314115:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00060 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00083
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PROKR2 | - | - |
GRCh38 GRCh37 |
147 | 183 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Conflicting interpretations of pathogenicity (9) |
criteria provided, conflicting classifications
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Mar 26, 2024 | RCV000022408.22 | |
Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
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Aug 25, 2023 | RCV000498536.30 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jul 17, 2023 | RCV003415639.4 | |
Uncertain significance (1) |
no assertion criteria provided
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Mar 8, 2021 | RCV001849252.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 11, 2019 | RCV002254257.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 1, 2023 | RCV003991566.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Aug 07, 2018)
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criteria provided, single submitter
Method: clinical testing
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Kallmann syndrome 3
Affected status: no
Allele origin:
inherited
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Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000845430.1
First in ClinVar: Nov 03, 2018 Last updated: Nov 03, 2018 |
Number of individuals with the variant: 1
Sex: female
Geographic origin: Iran
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Pathogenic
(Jun 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV001752702.1
First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021 |
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Likely pathogenic
(Sep 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002579511.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Number of individuals with the variant: 1
Sex: male
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Likely pathogenic
(Jun 11, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: no
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002766826.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as likely pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of … (more)
Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as likely pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene (PMID:18826963). (N) 0104 - Dominant Negative is a mechanism of disease for this gene (PMID:29161432). (N) 0108 - This gene is known to be associated with both recessive and dominant disease, where recessive is more penetrant and severe (OMIM). (N) 0112 - Variants in this gene are known to have reduced penetrance for heterozygous carriers (OMIM). (N) 0200 - Variant is predicted to result in a missense amino acid change from arginine to histidine. THis variant is in exon 2 of the PROKR2 gene. (N) 0251 - Variant is heterozygous. (N) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (166 heterozygote, 2 homozygotes). (N) 0310 - Variant is present in gnomAD >=0.001 and 0.01 for a dominant condition (212 heterozygote, 0 homozygotes). (N) 0502 - Missense variant with conflicting in silico predictions and/or uninformative conservation. (N) 0600 - Variant is located in an annotated domain or motif, (7 transmembrane receptor; PDB). (N) 0703 - Comparable variants have moderate previous evidence for pathogenicity. Alternative changes (p.Arg85Leu, p.Arg85Gly) have been reported as likely benign but mostly pathogenic (ClinVar, PMID:29161432, PMID:20022991, PMID:31093944) in patients with Kallman syndrome. An additional alternative change (p.Arg85Cys) (P) 0802 - Moderate previous evidence of pathogenicity. This variant has been described as both VUS and pathogenic (ClinVar, LOVD). However, it has been reported in multiple unrelated heterozygous patients as well as a homozygote patient, with Kallman syndrome (PMID:29161432, PMID:17054399, PMID:22466334). (P) 1002 - Moderate functional evidence supporting abnormal protein function. Functional analysis showed a significant reduction in calcium mobilization, MAPK signal activation and whole cell protein expression (PMID:18826963, PMID: 18682503). (P) 1208 – Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign (less)
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Uncertain significance
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV002151784.2
First in ClinVar: Mar 28, 2022 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 85 of the PROKR2 protein (p.Arg85His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 85 of the PROKR2 protein (p.Arg85His). This variant is present in population databases (rs74315418, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Kallmann syndrome (PMID: 17054399). ClinVar contains an entry for this variant (Variation ID: 3451). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PROKR2 function (PMID: 18826963, 22745195, 24830383, 29161432). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
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Likely pathogenic
(Jul 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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PROKR2-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004114853.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The PROKR2 c.254G>A variant is predicted to result in the amino acid substitution p.Arg85His. This variant has been reported in the heterozygous and homozygous states … (more)
The PROKR2 c.254G>A variant is predicted to result in the amino acid substitution p.Arg85His. This variant has been reported in the heterozygous and homozygous states in many individuals with Kallmann syndrome and hypogonadotropic hypogonadism (Dodé et al 2006. PubMed ID: 17054399; Sarfati et al. 2010. PubMed ID: 20022991; Table S3, Miraoui et al. 2013. PubMed ID: 23643382; Choi et al. 2015. PubMed ID: 26207952; Hacquart et al. 2017. PubMed ID: 28807454; Kaluzna et al. 2021. PubMed ID: 34198905; Cho et al. 2021. PubMed ID: 33775534). This variant has also been reported in individuals with hypopituitarism and hypothalamic amenorrhea (Reynaud et al. 2012. PubMed ID: 22466334; Jullien et al. 2020. PubMed ID: 33098107; Caronia et al. 2011. PubMed ID: 21247312; Delaney et al. 2020. PubMed ID: 32870266). Functional studies showed that this variant impairs Gq-dependent signaling activity and decreases PROKR2 expression when tested alone, but when co-transfected with wild type, only 2 of 3 signaling assays showed loss of function (Monnier et al. 2009. PubMed ID: 18826963; Caronia et al. 2011. PubMed ID: 21247312; Reynaud et al. 2012. PubMed ID: 22466334; Cox et al. 2018. PubMed ID: 29161432). This variant is reported in 0.12% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/20-5294762-C-T), and is present in asymptomatic family members (Caronia et al. 2011. PubMed ID: 21247312; Reynaud et al. 2012. PubMed ID: 22466334). Based on the available evidence, this variant is classified as likely pathogenic. (less)
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Uncertain significance
(May 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001153424.21
First in ClinVar: Feb 03, 2020 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 1
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Uncertain significance
(Nov 17, 2015)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000337346.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 2
Sex: mixed
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Pathogenic
(Sep 11, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadism with anosmia
Affected status: yes
Allele origin:
germline
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Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital
Accession: SCV002525580.1
First in ClinVar: Jun 11, 2022 Last updated: Jun 11, 2022 |
Comment:
This is a recurrent pathogenic variant that is known to exhibit incomplete penetrance and variable expressivity. This change has been reported in individuals with Kallmann … (more)
This is a recurrent pathogenic variant that is known to exhibit incomplete penetrance and variable expressivity. This change has been reported in individuals with Kallmann syndrome (KS), normosmic isolated gonadotropin-releasing hormone deficiency (IGD), anosomia, hypopituitarism, and hypothalamic amenorrhea; but is also present in many phenotypically normal individuals (PMID: 23596439, PMID: 20022991, PMID: 21247312, PMID: 22319038, PMID: 22466334, PMID: 23082007, PMID: 23643382). The c.254G>A variant, located in exon 2 of PROKR2, substitutes the arginine with histidine at position 85 of the protein. This variant is found in individuals with European ancestry with an allele frequency of ~0.12% (161/129,188 alleles) in the Genome Aggregation Database. This frequency is due to a common founder allele (PMID: 26207952). The p.Arg85His change has been demonstrated to cause a loss of function in in vitro assays (PMID: 18826963, PMID: 29161432). (less)
Clinical Features:
Penoscrotal transposition (present) , Hypospadias (present) , Chordee (present)
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Likely pathogenic
(Sep 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV002576400.1
First in ClinVar: Oct 01, 2022 Last updated: Oct 01, 2022 |
Comment:
_x000D_ Criteria applied: PS3, PM5
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Pathogenic
(Nov 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009987.3
First in ClinVar: Nov 06, 2021 Last updated: Jul 16, 2023 |
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Likely pathogenic
(Aug 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000589350.6
First in ClinVar: Aug 20, 2017 Last updated: Aug 31, 2023 |
Comment:
Published functional studies demonstrate impaired G-protein signaling (Monnier et al., 2009; Sbai et al. 2014); In silico analysis, which includes protein predictors and evolutionary conservation, … (more)
Published functional studies demonstrate impaired G-protein signaling (Monnier et al., 2009; Sbai et al. 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21247312, 23643382, 21858136, 24830383, 22745195, 22319038, 26207952, 22466334, 29161432, 18826963, 32870266, 34198905, 30487145, 28807454, 34426522, 33775534, 35669683, 33098107, 17054399, 36694982, 31093944, 35236788, 18682503, 37122876, 37321569, 37019085, 37338295, 20022991) (less)
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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HYPOGONADOTROPIC HYPOGONADISM 3 WITH OR WITHOUT ANOSMIA
Affected status: yes
Allele origin:
germline
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Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV004046326.1
First in ClinVar: Oct 21, 2023 Last updated: Oct 21, 2023 |
Comment:
This variant has been previously reported in the literature in association with a range of phenotypes that include septo-optic dysplasia (SOD), combined pituitary hormone deficiency … (more)
This variant has been previously reported in the literature in association with a range of phenotypes that include septo-optic dysplasia (SOD), combined pituitary hormone deficiency (CPHD), hypothalamic amenorrhea, Hypopituitarism with pituitary stalk interruption, Hirschsprung disease, and Kallman syndrome (PMID: 22319038, 21247312, 21858136, 22466334, 20022991, 17054399, 30487145). Inheritance studies showed that the c.254G>A (p.Arg85His) variant is often inherited from an unaffected parent and/or detected in other unaffected family members, which suggests incomplete penetrance (PMID: 21247312, 22466334). Additionally, one individual was reported with the c.254G>A (p.Arg85His) variant and another variant in a gene associated with pituitary hormone deficiency (PMID: 22319038). Functional studies showed that the presence of this variant resulted in a mild damaging effect on receptor signaling activity (PMID: 21247312, 24830383, 29161432, 18826963). However, recent functional studies suggest the c.254G>A (p.Arg85His) variant is only damaging in the homozygous state (PMID: 29161432). A different nucleotide change at the same position (c.254G>T, p.Arg85Leu) has been reported as a heterozygous change in individuals with Kallman syndrome, combined pituitary hormone deficiency, GH deficiency, TSH deficiency and ACTH deficiency affected individuals (PMID: 23386640, 20022991). The c.254G>A (p.Arg85His) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.075% (212/282884) and is absent in the homozygous state. The c.254G>A (p.Arg85His) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.254G>A (p.Arg85His) variant is classified as Likely Pathogenic. (less)
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Pathogenic
(Sep 01, 2023)
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criteria provided, single submitter
Method: research
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Male infertility with azoospermia or oligozoospermia due to single gene mutation
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Laan Lab, Human Genetics Research Group, University of Tartu
Accession: SCV004239171.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Observation 1:
Sex: male
Observation 2:
Sex: male
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Uncertain significance
(Mar 26, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004807076.1
First in ClinVar: Apr 06, 2024 Last updated: Apr 06, 2024 |
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Pathogenic
(Jan 01, 2009)
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no assertion criteria provided
Method: literature only
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HYPOGONADOTROPIC HYPOGONADISM 3 WITH ANOSMIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000043093.4
First in ClinVar: Apr 04, 2013 Last updated: Jul 02, 2015 |
Comment on evidence:
In affected members of a family with Kallmann syndrome (HH3; 244200), Dode et al. (2006) identified heterozygosity for a 254G-A transition in exon 1 of … (more)
In affected members of a family with Kallmann syndrome (HH3; 244200), Dode et al. (2006) identified heterozygosity for a 254G-A transition in exon 1 of the PROKR2 gene, resulting in an arg85-to-his (R85H) substitution. They identified the same mutation in homozygous state in a sporadic case of Kallmann syndrome. Monnier et al. (2009) performed functional analysis of the R85H mutation in HEK293 cells and observed decreased signaling activity compared to wildtype. (less)
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Likely pathogenic
(Sep 26, 2019)
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no assertion criteria provided
Method: clinical testing
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Hypogonadotropic hypogonadism 3 with or without anosmia
Affected status: yes
Allele origin:
germline
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Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Accession: SCV001133174.1
First in ClinVar: Jan 06, 2020 Last updated: Jan 06, 2020 |
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Uncertain significance
(Mar 08, 2021)
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no assertion criteria provided
Method: literature only
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Amenorrhea
Affected status: yes
Allele origin:
unknown
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Yale Center for Mendelian Genomics, Yale University
Study: Yale Center for Mendelian Genomics
Accession: SCV002106805.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Increased Burden of Rare Sequence Variants in GnRH-Associated Genes in Women With Hypothalamic Amenorrhea. | Delaney A | The Journal of clinical endocrinology and metabolism | 2021 | PMID: 32870266 |
Genetic analysis of adult Slovenian patients with combined pituitary hormone deficiency. | Bajuk Studen K | Endocrine | 2019 | PMID: 31093944 |
Modeling mutant/wild-type interactions to ascertain pathogenicity of PROKR2 missense variants in patients with isolated GnRH deficiency. | Cox KH | Human molecular genetics | 2018 | PMID: 29161432 |
Biased signaling through G-protein-coupled PROKR2 receptors harboring missense mutations. | Sbai O | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2014 | PMID: 24830383 |
Evidence of the importance of the first intracellular loop of prokineticin receptor 2 in receptor function. | Abreu AP | Molecular endocrinology (Baltimore, Md.) | 2012 | PMID: 22745195 |
PROKR2 variants in multiple hypopituitarism with pituitary stalk interruption. | Reynaud R | The Journal of clinical endocrinology and metabolism | 2012 | PMID: 22466334 |
A comparative phenotypic study of kallmann syndrome patients carrying monoallelic and biallelic mutations in the prokineticin 2 or prokineticin receptor 2 genes. | Sarfati J | The Journal of clinical endocrinology and metabolism | 2010 | PMID: 20022991 |
PROKR2 missense mutations associated with Kallmann syndrome impair receptor signalling activity. | Monnier C | Human molecular genetics | 2009 | PMID: 18826963 |
Loss-of-function mutations in the genes encoding prokineticin-2 or prokineticin receptor-2 cause autosomal recessive Kallmann syndrome. | Abreu AP | The Journal of clinical endocrinology and metabolism | 2008 | PMID: 18682503 |
Kallmann syndrome: mutations in the genes encoding prokineticin-2 and prokineticin receptor-2. | Dodé C | PLoS genetics | 2006 | PMID: 17054399 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PROKR2 | - | - | - | - |
- | - | - | - | DOI: 10.1016/j.ajhg.2024.03.013 |
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Text-mined citations for rs74315418 ...
HelpRecord last updated Apr 15, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.