ClinVar Genomic variation as it relates to human health
NM_001032221.6(STXBP1):c.1099C>T (p.Arg367Ter)
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001032221.6(STXBP1):c.1099C>T (p.Arg367Ter)
Variation ID: 207429 Accession: VCV000207429.21
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q34.11 9: 127673250 (GRCh38) [ NCBI UCSC ] 9: 130435529 (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 May 29, 2016 Nov 3, 2024 Dec 25, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001032221.6:c.1099C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001027392.1:p.Arg367Ter nonsense NM_003165.6:c.1099C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_003156.1:p.Arg367Ter nonsense NM_001374306.2:c.1090C>T NP_001361235.1:p.Arg364Ter nonsense NM_001374307.2:c.1057C>T NP_001361236.1:p.Arg353Ter nonsense NM_001374308.2:c.1057C>T NP_001361237.1:p.Arg353Ter nonsense NM_001374309.2:c.1057C>T NP_001361238.1:p.Arg353Ter nonsense NM_001374310.2:c.1057C>T NP_001361239.1:p.Arg353Ter nonsense NM_001374311.2:c.1057C>T NP_001361240.1:p.Arg353Ter nonsense NM_001374312.2:c.1057C>T NP_001361241.1:p.Arg353Ter nonsense NM_001374313.2:c.1099C>T NP_001361242.1:p.Arg367Ter nonsense NM_001374314.1:c.1099C>T NP_001361243.1:p.Arg367Ter nonsense NM_001374315.2:c.991C>T NP_001361244.1:p.Arg331Ter nonsense NC_000009.12:g.127673250C>T NC_000009.11:g.130435529C>T NG_016623.1:g.66044C>T - Protein change
- R367*, R331*, R353*, R364*
- Other names
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p.R367*:CGA>TGA
- Canonical SPDI
- NC_000009.12:127673249: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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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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STXBP1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1086 | 1181 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Pathogenic (1) |
criteria provided, single submitter
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Jun 20, 2022 | RCV000189611.5 | |
Pathogenic (1) |
criteria provided, single submitter
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Nov 16, 2016 | RCV000416987.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 25, 2023 | RCV000477371.13 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 10, 2020 | RCV001260836.3 | |
Pathogenic (1) |
no assertion criteria provided
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Nov 10, 2017 | RCV001265514.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 4, 2021 | RCV001807119.3 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Mar 5, 2022 | RCV001336021.8 |
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
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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
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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
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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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Pathogenic
(Nov 16, 2016)
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criteria provided, single submitter
Method: clinical testing
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Epileptic encephalopathy
Affected status: yes
Allele origin:
de novo
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Neurogenetics Laboratory - MEYER, AOU Meyer
Accession: SCV000494527.1
First in ClinVar: Feb 12, 2017 Last updated: Feb 12, 2017 |
Family history: no
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Pathogenic
(Jun 06, 2016)
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criteria provided, single submitter
Method: clinical testing
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Early infantile epileptic encephalopathy with suppression bursts
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000711983.2
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
The p.Arg367X variant in STXBP1 has been previously identified de novo in 2 indi viduals with features of STXBP1 encephalopathy (Stamberger 2016, Yamashita 2016) , … (more)
The p.Arg367X variant in STXBP1 has been previously identified de novo in 2 indi viduals with features of STXBP1 encephalopathy (Stamberger 2016, Yamashita 2016) , and was absent from large population studies. This nonsense variant leads to a premature termination codon at position 367, which is predicted to lead to a tr uncated or absent protein. Heterozygous loss-of-function variants in the STXBP1 gene are causative for STXBP1 encephalopathy. In summary, this variant meets our criteria to be classified as pathogenic for STXBP1 encephalopathy in an autosom al dominant manner based upon its predicted impact to the protein, de novo occur rences in affected individuals and absence in the general population. (less)
Number of individuals with the variant: 1
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Pathogenic
(Dec 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Early infantile epileptic encephalopathy with suppression bursts
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000547211.5
First in ClinVar: Apr 17, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg367*) in the STXBP1 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg367*) in the STXBP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in STXBP1 are known to be pathogenic (PMID: 20887364, 26384463). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Ohtahara syndrome or early infantile epileptic encephalopathy (PMID: 26918652, 27159321). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 207429). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jun 20, 2022)
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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: SCV000243256.14
First in ClinVar: Aug 07, 2015 Last updated: Nov 03, 2024 |
Comment:
Nonsense variant predicted to result in protein truncation or nonsense-mediated decay in a gene for which loss of function is a known mechanism of disease; … (more)
Nonsense variant predicted to result in protein truncation or nonsense-mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26865513, 23593750, 28944233, 25533962, 27159321, 26918652, 29538625, 30187003, 28135719, 31344879, 31785789, 33726816, 31440721, 28191890, 29655203, 36480001, 33057194, 36939041, 36801247, 36475376, 35982159) (less)
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Pathogenic
(Sep 10, 2020)
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criteria provided, single submitter
Method: clinical testing
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Intellectual disability
Affected status: yes
Allele origin:
de novo
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Diagnostic Laboratory, Strasbourg University Hospital
Accession: SCV001437932.1
First in ClinVar: Oct 10, 2020 Last updated: Oct 10, 2020 |
Method: targeted next-gen sequencing
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Pathogenic
(Dec 01, 2018)
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criteria provided, single submitter
Method: clinical testing
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Developmental and epileptic encephalopathy, 4
Affected status: yes
Allele origin:
de novo
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Baylor Genetics
Accession: SCV001529296.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease-causing [PMID 25533962, 28135719, 27159321]
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Pathogenic
(Dec 04, 2021)
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criteria provided, single submitter
Method: clinical testing
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Cerebellar ataxia
Tremor Moderate global developmental delay
Affected status: yes
Allele origin:
de novo
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Institute of Human Genetics, University Hospital Muenster
Accession: SCV002054113.1
First in ClinVar: Jan 12, 2022 Last updated: Jan 12, 2022 |
Comment:
ACMG categories: PVS1,PS2,PM2,PP3,PP5
Number of individuals with the variant: 1
Age: 0-9 years
Sex: female
Tissue: blood
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Pathogenic
(Mar 05, 2022)
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criteria provided, single submitter
Method: clinical testing
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Developmental and epileptic encephalopathy, 4
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002107137.2
First in ClinVar: Mar 28, 2022 Last updated: Apr 02, 2022 |
Comment:
The c.1099C>T;p.(Arg367*) variant creates a premature translational stop signal in the STXBP1 gene. It is expected to result in an absent or disrupted protein product … (more)
The c.1099C>T;p.(Arg367*) variant creates a premature translational stop signal in the STXBP1 gene. It is expected to result in an absent or disrupted protein product - PVS1. Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 26918652) - PS3_supporting. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 207429; PMID: 28135719; PMID: 27159321; PMID: 26918652) - PS4. This variant is not present in population databases (rs796053366- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 27159321; 26918652) - PM6. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 1
Sex: female
Geographic origin: Brazil
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Developmental and epileptic encephalopathy, 4
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV002820125.1
First in ClinVar: Jan 21, 2023 Last updated: Jan 21, 2023 |
Comment:
The stop gained p.R367* in STXBP1 (NM_003165.6) has been previously identified de novo in 2 individuals with features of STXBP1 encephalopathy (Stamberger 2016, Yamashita 2016). … (more)
The stop gained p.R367* in STXBP1 (NM_003165.6) has been previously identified de novo in 2 individuals with features of STXBP1 encephalopathy (Stamberger 2016, Yamashita 2016). Heterozygous loss-of-function variants in the STXBP1 gene are causative for STXBP1 encephalopathy. The variant has been reported to ClinVar as Pathogenic. The p.R367* variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation. The p.R367* variant is a loss of function variant in the gene STXBP1, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_003156.1:p.M1Lfs*604 and 119 others. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Global developmental delay (present) , Cerebellar ataxia (present) , Broad-based gait (present) , Hyperactivity (present) , Hypotonia (present)
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Pathogenic
(Nov 10, 2017)
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no assertion criteria provided
Method: provider interpretation
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Infantile epilepsy syndrome
Affected status: yes
Allele origin:
unknown
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GenomeConnect - Simons Searchlight
Accession: SCV001443658.1
First in ClinVar: Nov 21, 2020 Last updated: Nov 21, 2020 |
Comment:
Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2017-11-10 and interpreted as Pathogenic. Variant was initially … (more)
Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2017-11-10 and interpreted as Pathogenic. Variant was initially reported on 2013-01-14 by GTR ID of laboratory name 26957. The reporting laboratory might also submit to ClinVar. (less)
Clinical Features:
Autistic behavior (present) , Neonatal seizure (present) , Neonatal hypotonia (present) , Abnormality of vision (present) , Myopia (disease) (present) , Nystagmus (present) , Ptosis … (more)
Autistic behavior (present) , Neonatal seizure (present) , Neonatal hypotonia (present) , Abnormality of vision (present) , Myopia (disease) (present) , Nystagmus (present) , Ptosis (present) , Clumsiness (present) , Generalized hypotonia (present) , Seizures (present) , Generalized tonic-clonic seizures (present) , Absence seizures (present) , Focal seizures with impairment of consciousness or awareness (present) , Focal seizures without impairment of consciousness or awareness (present) , Gastroesophageal reflux (present) , Constipation (present) , Otitis media (present) , Abnormality of the skin (present) , Eczema (present) , Allergy (present) , Food allergy (present) , Allergic rhinitis (present) , Abnormality of the cardiovascular system (present) (less)
Age: 0-9 years
Sex: female
Testing laboratory: GeneDx
Date variant was reported to submitter: 2013-01-14
Testing laboratory interpretation: Pathogenic
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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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Prevalence and architecture of de novo mutations in developmental disorders. | Deciphering Developmental Disorders Study | Nature | 2017 | PMID: 28135719 |
Whole exome sequencing in patients with white matter abnormalities. | Vanderver A | Annals of neurology | 2016 | PMID: 27159321 |
Mislocalization of syntaxin-1 and impaired neurite growth observed in a human iPSC model for STXBP1-related epileptic encephalopathy. | Yamashita S | Epilepsia | 2016 | PMID: 26918652 |
STXBP1 encephalopathy: A neurodevelopmental disorder including epilepsy. | Stamberger H | Neurology | 2016 | PMID: 26865513 |
Loss-of-function mutations of STXBP1 in patients with epileptic encephalopathy. | Yamamoto T | Brain & development | 2016 | PMID: 26384463 |
Large-scale discovery of novel genetic causes of developmental disorders. | Deciphering Developmental Disorders Study | Nature | 2015 | PMID: 25533962 |
STXBP1 mutations in early infantile epileptic encephalopathy with suppression-burst pattern. | Saitsu H | Epilepsia | 2010 | PMID: 20887364 |
Text-mined citations for rs796053366 ...
HelpRecord last updated Nov 03, 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.