ClinVar Genomic variation as it relates to human health
NM_001077207.4(SEC31A):c.3128C>T (p.Pro1043Leu)
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_001077207.4(SEC31A):c.3128C>T (p.Pro1043Leu)
Variation ID: 3159355 Accession: VCV003159355.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4q21.22 4: 82827532 (GRCh38) [ NCBI UCSC ] 4: 83748685 (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 1, 2024 May 1, 2024 Jan 30, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001077207.4:c.3128C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001070675.1:p.Pro1043Leu missense NM_001077206.4:c.2786C>T NP_001070674.1:p.Pro929Leu missense NM_001077208.4:c.3083C>T NP_001070676.1:p.Pro1028Leu missense NM_001191049.2:c.3068C>T NP_001177978.1:p.Pro1023Leu missense NM_001300744.3:c.2669C>T NP_001287673.1:p.Pro890Leu missense NM_001300745.3:c.2966C>T NP_001287674.1:p.Pro989Leu missense NM_001318119.2:c.3083C>T NP_001305048.1:p.Pro1028Leu missense NM_001318120.2:c.3128C>T NP_001305049.1:p.Pro1043Leu missense NM_001400154.1:c.3221C>T NP_001387083.1:p.Pro1074Leu missense NM_001400155.1:c.3221C>T NP_001387084.1:p.Pro1074Leu missense NM_001400156.1:c.3176C>T NP_001387085.1:p.Pro1059Leu missense NM_001400157.1:c.3167C>T NP_001387086.1:p.Pro1056Leu missense NM_001400158.1:c.3167C>T NP_001387087.1:p.Pro1056Leu missense NM_001400159.1:c.3167C>T NP_001387088.1:p.Pro1056Leu missense NM_001400160.1:c.3143C>T NP_001387089.1:p.Pro1048Leu missense NM_001400161.1:c.3143C>T NP_001387090.1:p.Pro1048Leu missense NM_001400162.1:c.3137C>T NP_001387091.1:p.Pro1046Leu missense NM_001400164.1:c.3128C>T NP_001387093.1:p.Pro1043Leu missense NM_001400165.1:c.3128C>T NP_001387094.1:p.Pro1043Leu missense NM_001400166.1:c.3128C>T NP_001387095.1:p.Pro1043Leu missense NM_001400167.1:c.3104C>T NP_001387096.1:p.Pro1035Leu missense NM_001400168.1:c.3104C>T NP_001387097.1:p.Pro1035Leu missense NM_001400180.1:c.3089C>T NP_001387109.1:p.Pro1030Leu missense NM_001400184.1:c.3089C>T NP_001387113.1:p.Pro1030Leu missense NM_001400186.1:c.3089C>T NP_001387115.1:p.Pro1030Leu missense NM_001400188.1:c.3089C>T NP_001387117.1:p.Pro1030Leu missense NM_001400190.1:c.3083C>T NP_001387119.1:p.Pro1028Leu missense NM_001400191.1:c.3083C>T NP_001387120.1:p.Pro1028Leu missense NM_001400193.1:c.3083C>T NP_001387122.1:p.Pro1028Leu missense NM_001400194.1:c.3128C>T NP_001387123.1:p.Pro1043Leu missense NM_001400197.1:c.3050C>T NP_001387126.1:p.Pro1017Leu missense NM_001400198.1:c.3050C>T NP_001387127.1:p.Pro1017Leu missense NM_001400200.1:c.3050C>T NP_001387129.1:p.Pro1017Leu missense NM_001400202.1:c.3050C>T NP_001387131.1:p.Pro1017Leu missense NM_001400203.1:c.3050C>T NP_001387132.1:p.Pro1017Leu missense NM_001400204.1:c.3044C>T NP_001387133.1:p.Pro1015Leu missense NM_001400205.1:c.3044C>T NP_001387134.1:p.Pro1015Leu missense NM_001400206.1:c.3044C>T NP_001387135.1:p.Pro1015Leu missense NM_001400207.1:c.3011C>T NP_001387136.1:p.Pro1004Leu missense NM_001400208.1:c.3083C>T NP_001387137.1:p.Pro1028Leu missense NM_001400209.1:c.3011C>T NP_001387138.1:p.Pro1004Leu missense NM_001400210.1:c.3005C>T NP_001387139.1:p.Pro1002Leu missense NM_001400211.1:c.3005C>T NP_001387140.1:p.Pro1002Leu missense NM_001400212.1:c.3068C>T NP_001387141.1:p.Pro1023Leu missense NM_001400213.1:c.2966C>T NP_001387142.1:p.Pro989Leu missense NM_001400214.1:c.3113C>T NP_001387143.1:p.Pro1038Leu missense NM_001400215.1:c.2849C>T NP_001387144.1:p.Pro950Leu missense NM_001400216.1:c.3044C>T NP_001387145.1:p.Pro1015Leu missense NM_001400217.1:c.2786C>T NP_001387146.1:p.Pro929Leu missense NM_001400218.1:c.2762C>T NP_001387147.1:p.Pro921Leu missense NM_001400219.1:c.2786C>T NP_001387148.1:p.Pro929Leu missense NM_001400220.1:c.2786C>T NP_001387149.1:p.Pro929Leu missense NM_001400221.1:c.2708C>T NP_001387150.1:p.Pro903Leu missense NM_001400222.1:c.2708C>T NP_001387151.1:p.Pro903Leu missense NM_001400223.1:c.2669C>T NP_001387152.1:p.Pro890Leu missense NM_001400224.1:c.2654C>T NP_001387153.1:p.Pro885Leu missense NM_016211.5:c.3011C>T NP_057295.2:p.Pro1004Leu missense NC_000004.12:g.82827532G>A NC_000004.11:g.83748685G>A NG_029569.3:g.78040C>T - Protein change
- P1028L, P1035L, P1038L, P1074L, P929L, P1015L, P1017L, P1043L, P1056L, P1004L, P1030L, P1048L, P1059L, P885L, P989L, P1002L, P1023L, P1046L, P890L, P903L, P921L, P950L
- Other names
- NM_014933.3:c.3128C>T
- Canonical SPDI
- NC_000004.12:82827531: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
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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
Help
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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SEC31A | - | - |
GRCh38 GRCh37 |
92 | 131 |
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
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
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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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Uncertain significance (1) |
criteria provided, single submitter
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Jan 30, 2024 | RCV004447710.1 |
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
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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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Uncertain significance
(Jan 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV004944810.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.3128C>T (p.P1043L) alteration is located in exon 24 (coding exon 23) of the SEC31A gene. This alteration results from a C to T substitution … (more)
The c.3128C>T (p.P1043L) alteration is located in exon 24 (coding exon 23) of the SEC31A gene. This alteration results from a C to T substitution at nucleotide position 3128, causing the proline (P) at amino acid position 1043 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
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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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated May 08, 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.