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NM_000038.6(APC):c.44C>T (p.Ala15Val) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 6, 2015
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:
RCV000485888.1

Allele description [Variation Report for NM_000038.6(APC):c.44C>T (p.Ala15Val)]

NM_000038.6(APC):c.44C>T (p.Ala15Val)

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.44C>T (p.Ala15Val)
HGVS:
  • NC_000005.10:g.112754934C>T
  • NG_008481.4:g.67414C>T
  • NM_000038.6:c.44C>TMANE SELECT
  • NM_001127510.3:c.44C>T
  • NM_001127511.3:c.166-11392C>T
  • NM_001354895.2:c.44C>T
  • NM_001354896.2:c.44C>T
  • NM_001354897.2:c.166-11392C>T
  • NM_001354898.2:c.61-11392C>T
  • NM_001354899.2:c.44C>T
  • NM_001354900.2:c.-42-11392C>T
  • NM_001354901.2:c.-42-11392C>T
  • NM_001354902.2:c.166-11392C>T
  • NM_001354903.2:c.44C>T
  • NM_001354904.2:c.61-11392C>T
  • NM_001354905.2:c.-42-11392C>T
  • NM_001354906.2:c.-992C>T
  • NP_000029.2:p.Ala15Val
  • NP_001120982.1:p.Ala15Val
  • NP_001341824.1:p.Ala15Val
  • NP_001341825.1:p.Ala15Val
  • NP_001341828.1:p.Ala15Val
  • NP_001341832.1:p.Ala15Val
  • LRG_130:g.67414C>T
  • NC_000005.9:g.112090631C>T
  • NM_000038.5:c.44C>T
Protein change:
A15V
Links:
dbSNP: rs1064793466
NCBI 1000 Genomes Browser:
rs1064793466
Molecular consequence:
  • NM_001354906.2:c.-992C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001127511.3:c.166-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354897.2:c.166-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354898.2:c.61-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354900.2:c.-42-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354901.2:c.-42-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354902.2:c.166-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354904.2:c.61-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354905.2:c.-42-11392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000038.6:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000566193GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Apr 6, 2015) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000566193.4

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

Description

This variant is denoted APC c.44C>T at the cDNA level, p.Ala15Val (A15V) at the protein level, and results in the change of an Alanine to a Valine (GCA>GTA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. APC Ala15Val was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Alanine and Valine share similar properties, this is considered a conservative amino acid substitution. APC Ala15Val occurs at a position that is conserved across species and is located within the oligomerization domain (Azzopardi 2008). Protein-based in silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Multiple splicing models predict gain of a cryptic splice donor site upstream of the natural site; however these models predict no change to the natural splice donor site. In the absence of RNA or functional studies, the actual effect of this variant is unknown. Based on currently available information, it is unclear whether APC Ala15Val is pathogenic or benign. We consider it to be a variant of uncertain significance.

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

Last Updated: Nov 24, 2024