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NM_000038.6(APC):c.5981A>T (p.Asp1994Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 2, 2021)
Last evaluated:
Oct 5, 2020
Accession:
VCV000236626.9
Variation ID:
236626
Description:
single nucleotide variant
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NM_000038.6(APC):c.5981A>T (p.Asp1994Val)

Allele ID
239596
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112841575 (GRCh38) GRCh38 UCSC
5: 112177272 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_130:g.154055A>T
NC_000005.10:g.112841575A>T
NC_000005.9:g.112177272A>T
... more HGVS
Protein change
D1976V, D1994V, D1834V, D1903V, D1953V, D1966V, D1868V, D1935V, D1969V, D1711V, D1893V, D2004V, D2012V
Other names
-
Canonical SPDI
NC_000005.10:112841574:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA043598
dbSNP: rs774815653
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Oct 5, 2020 RCV000227428.8
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations May 18, 2020 RCV000571074.5
Uncertain significance 1 no assertion criteria provided Aug 15, 2019 RCV001589165.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APC Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
8948 8982

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 05, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000282789.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces aspartic acid with valine at codon 1994 of the APC protein (p.Asp1994Val). The aspartic acid residue is moderately conserved and there … (more)
Uncertain significance
(Aug 03, 2017)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: unknown
Counsyl
Accession: SCV000785373.2
Submitted: (Jun 20, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(May 30, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903336.2
Submitted: (May 19, 2020)
Evidence details
Likely benign
(May 18, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000675863.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);RNA Studies;Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene
Uncertain significance
(Aug 15, 2019)
no assertion criteria provided
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001825747.1
Submitted: (Sep 02, 2021)
Evidence details
Comment:
Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Missense mutations in MLH1, MSH2, KRAS, and APC genes in colorectal cancer patients in Malaysia. Abdul Murad NA Digestive diseases and sciences 2012 PMID: 22669205

Text-mined citations for rs774815653...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 07, 2021