NM_000038.6(APC):c.6639G>A (p.Met2213Ile) AND not provided

Clinical significance:Likely benign (Last evaluated: Dec 15, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000484737.3

Allele description [Variation Report for NM_000038.6(APC):c.6639G>A (p.Met2213Ile)]

NM_000038.6(APC):c.6639G>A (p.Met2213Ile)

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.6639G>A (p.Met2213Ile)
HGVS:
  • NC_000005.10:g.112842233G>A
  • NG_008481.4:g.154713G>A
  • NM_000038.6:c.6639G>AMANE SELECT
  • NM_001127510.3:c.6639G>A
  • NM_001127511.3:c.6585G>A
  • NM_001354895.2:c.6639G>A
  • NM_001354896.2:c.6693G>A
  • NM_001354897.2:c.6669G>A
  • NM_001354898.2:c.6564G>A
  • NM_001354899.2:c.6555G>A
  • NM_001354900.2:c.6516G>A
  • NM_001354901.2:c.6462G>A
  • NM_001354902.2:c.6366G>A
  • NM_001354903.2:c.6336G>A
  • NM_001354904.2:c.6261G>A
  • NM_001354905.2:c.6159G>A
  • NM_001354906.2:c.5790G>A
  • NP_000029.2:p.Met2213Ile
  • NP_001120982.1:p.Met2213Ile
  • NP_001120983.2:p.Met2195Ile
  • NP_001341824.1:p.Met2213Ile
  • NP_001341825.1:p.Met2231Ile
  • NP_001341826.1:p.Met2223Ile
  • NP_001341827.1:p.Met2188Ile
  • NP_001341828.1:p.Met2185Ile
  • NP_001341829.1:p.Met2172Ile
  • NP_001341830.1:p.Met2154Ile
  • NP_001341831.1:p.Met2122Ile
  • NP_001341832.1:p.Met2112Ile
  • NP_001341833.1:p.Met2087Ile
  • NP_001341834.1:p.Met2053Ile
  • NP_001341835.1:p.Met1930Ile
  • LRG_130:g.154713G>A
  • NC_000005.9:g.112177930G>A
  • NM_000038.5:c.6639G>A
  • p.M2213I
Protein change:
M1930I
Links:
dbSNP: rs35540155
NCBI 1000 Genomes Browser:
rs35540155
Molecular consequence:
  • NM_000038.6:c.6639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.6639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.6585G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.6639G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.6693G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.6669G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.6564G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.6555G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.6516G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.6462G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.6366G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.6336G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.6261G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.6159G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.5790G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000566001GeneDxcriteria provided, single submitter
Likely benign
(Dec 15, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000566001.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25980754, 24123366, 21153778, 31159747)

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

Last Updated: Nov 27, 2021

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