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NM_000038.6(APC):c.4913T>C (p.Met1638Thr) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 19, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004525836.4

Allele description [Variation Report for NM_000038.6(APC):c.4913T>C (p.Met1638Thr)]

NM_000038.6(APC):c.4913T>C (p.Met1638Thr)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.4913T>C (p.Met1638Thr)
HGVS:
  • NC_000005.10:g.112840507T>C
  • NG_008481.4:g.152987T>C
  • NM_000038.6:c.4913T>CMANE SELECT
  • NM_001127510.3:c.4913T>C
  • NM_001127511.3:c.4859T>C
  • NM_001354895.2:c.4913T>C
  • NM_001354896.2:c.4967T>C
  • NM_001354897.2:c.4943T>C
  • NM_001354898.2:c.4838T>C
  • NM_001354899.2:c.4829T>C
  • NM_001354900.2:c.4790T>C
  • NM_001354901.2:c.4736T>C
  • NM_001354902.2:c.4640T>C
  • NM_001354903.2:c.4610T>C
  • NM_001354904.2:c.4535T>C
  • NM_001354905.2:c.4433T>C
  • NM_001354906.2:c.4064T>C
  • NP_000029.2:p.Met1638Thr
  • NP_001120982.1:p.Met1638Thr
  • NP_001120983.2:p.Met1620Thr
  • NP_001341824.1:p.Met1638Thr
  • NP_001341825.1:p.Met1656Thr
  • NP_001341826.1:p.Met1648Thr
  • NP_001341827.1:p.Met1613Thr
  • NP_001341828.1:p.Met1610Thr
  • NP_001341829.1:p.Met1597Thr
  • NP_001341830.1:p.Met1579Thr
  • NP_001341831.1:p.Met1547Thr
  • NP_001341832.1:p.Met1537Thr
  • NP_001341833.1:p.Met1512Thr
  • NP_001341834.1:p.Met1478Thr
  • NP_001341835.1:p.Met1355Thr
  • LRG_130:g.152987T>C
  • NC_000005.9:g.112176204T>C
  • NM_000038.5:c.4913T>C
Protein change:
M1355T
Links:
dbSNP: rs201797422
NCBI 1000 Genomes Browser:
rs201797422
Molecular consequence:
  • NM_000038.6:c.4913T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.4913T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.4859T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.4913T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.4967T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.4943T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.4838T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.4829T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.4790T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.4736T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.4640T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.4610T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.4535T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.4433T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.4064T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000694063Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely benign
(Mar 19, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Population-based Screening for Hereditary Colorectal Cancer Variants in Japan.

Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, Takata S, Inai C, Aoi T, Mizukoshi M, Maejima K, Hirata M, Murakami Y, Kamatani Y, Kubo M, Akagi K, Matsuda K, Nakagawa H, Momozawa Y.

Clin Gastroenterol Hepatol. 2022 Sep;20(9):2132-2141.e9. doi: 10.1016/j.cgh.2020.12.007. Epub 2020 Dec 11.

PubMed [citation]
PMID:
33309985

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694063.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: APC c.4913T>C (p.Met1638Thr) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2.7e-05 in 1614138 control chromosomes, predominantly at a frequency of 0.0008 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 11 fold of the estimated maximal expected allele frequency for a pathogenic variant in APC causing Familial Adenomatous Polyposis phenotype (7.1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.4913T>C has been reported in the literature in individuals affected with Colorectal cancer (CRC) as well as unaffected control study individuals and authors classified this variant as benign (Fujita_2022). The following publication has been ascertained in the context of this evaluation (PMID: 33309985). ClinVar contains an entry for this variant (Variation ID: 231898). Based on the evidence outlined above, the variant was classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 19, 2025