ClinVar Genomic variation as it relates to human health
NM_138477.4(CDAN1):c.3389C>T (p.Pro1130Leu)
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_138477.4(CDAN1):c.3389C>T (p.Pro1130Leu)
Variation ID: 3177 Accession: VCV000003177.16
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 15q15.2 15: 42725550 (GRCh38) [ NCBI UCSC ] 15: 43017748 (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 Apr 4, 2013 Feb 14, 2024 Jun 23, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_138477.4:c.3389C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_612486.2:p.Pro1130Leu missense NC_000015.10:g.42725550G>A NC_000015.9:g.43017748G>A NG_012491.1:g.16670C>T LRG_1164:g.16670C>T LRG_1164t1:c.3389C>T LRG_1164p1:p.Pro1130Leu Q8IWY9:p.Pro1130Leu - Protein change
- P1130L
- Other names
- P1129L
- Canonical SPDI
- NC_000015.10:42725549:G:A
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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
Help
The frequency of the allele represented by this VCV record.
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
The Genome Aggregation Database (gnomAD) 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00005
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
Help
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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CDAN1 | - | - |
GRCh38 GRCh37 |
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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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Pathogenic (2) |
no assertion criteria provided
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Dec 1, 2002 | RCV000020959.8 | |
Pathogenic/Likely pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jun 23, 2022 | RCV001267935.7 | |
Pathogenic (2) |
criteria provided, single submitter
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Dec 27, 2021 | RCV001839408.4 |
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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Likely pathogenic
(Oct 26, 2021)
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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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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV002573755.1
First in ClinVar: Sep 24, 2022 Last updated: Sep 24, 2022 |
Comment:
PP3, PM2, PM3, PS4
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Pathogenic
(Dec 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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Anemia, congenital dyserythropoietic, type 1a
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV003820617.2
First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024 |
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Pathogenic
(Jun 23, 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: SCV003443459.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
This variant is present in population databases (rs80338699, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral … (more)
This variant is present in population databases (rs80338699, gnomAD 0.006%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1130 of the CDAN1 protein (p.Pro1130Leu). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 3177). This missense change has been observed in individual(s) with clinical features of congenital dyserythropoietic anemia (PMID: 28102861, 29031773, 29676459, 29936674, 33401150). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. (less)
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Pathogenic
(Oct 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001446452.1
First in ClinVar: Nov 28, 2020 Last updated: Nov 28, 2020 |
Clinical Features:
Anemia (present) , Macrocytic dyserythropoietic anemia (present)
Sex: male
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Pathogenic
(May 14, 2019)
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no assertion criteria provided
Method: clinical testing
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Anemia, congenital dyserythropoietic, type 1a
Affected status: yes
Allele origin:
paternal
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Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001190236.2
First in ClinVar: Oct 11, 2015 Last updated: Mar 02, 2022 |
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Pathogenic
(Dec 01, 2002)
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no assertion criteria provided
Method: literature only
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ANEMIA, CONGENITAL DYSERYTHROPOIETIC, TYPE Ia
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000023485.3
First in ClinVar: Apr 04, 2013 Last updated: Mar 18, 2023 |
Comment on evidence:
In a French Polynesian family with type Ia congenital dyserythropoietic anemia (CDAN1A; 224120), Dgany et al. (2002) identified a C-to-T transition at nucleotide 3503 in … (more)
In a French Polynesian family with type Ia congenital dyserythropoietic anemia (CDAN1A; 224120), Dgany et al. (2002) identified a C-to-T transition at nucleotide 3503 in the CDAN1 gene, resulting in a pro1129-to-leu substitution. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Congenital dyserythropoietic anemia, type I
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000041584.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 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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- | - | - | - | PMID: 12434312 |
- | - | - | - | PMID: 24196372 |
- | - | - | - | PMID: 28102861 |
- | - | - | - | PMID: 28755517 |
- | - | - | - | PMID: 29031773 |
- | - | - | - | PMID: 29676459 |
- | - | - | - | PMID: 29936674 |
- | - | - | - | PMID: 30836435 |
- | - | - | - | PMID: 33401150 |
- | - | - | - | PMID: 34782754 |
- | - | - | - | PMID: 20301759 |
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Text-mined citations for rs80338699 ...
HelpRecord last updated Mar 17, 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.