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NM_004360.5(CDH1):c.316A>G (p.Thr106Ala) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 14, 2017
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:
RCV000115861.2

Allele description [Variation Report for NM_004360.5(CDH1):c.316A>G (p.Thr106Ala)]

NM_004360.5(CDH1):c.316A>G (p.Thr106Ala)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.316A>G (p.Thr106Ala)
Other names:
p.T106A:ACC>GCC
HGVS:
  • NC_000016.10:g.68801822A>G
  • NG_008021.1:g.69531A>G
  • NM_001317184.2:c.316A>G
  • NM_001317185.2:c.-1300A>G
  • NM_001317186.2:c.-1504A>G
  • NM_004360.5:c.316A>GMANE SELECT
  • NP_001304113.1:p.Thr106Ala
  • NP_004351.1:p.Thr106Ala
  • LRG_301t1:c.316A>G
  • LRG_301:g.69531A>G
  • NC_000016.9:g.68835725A>G
  • NM_004360.3:c.316A>G
Protein change:
T106A
Links:
dbSNP: rs587780122
NCBI 1000 Genomes Browser:
rs587780122
Molecular consequence:
  • NM_001317185.2:c.-1300A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1504A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.316A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.316A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000149770GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jun 14, 2017) 		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, SCV000149770.13

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

Description

This variant is denoted CDH1 c.316A>G at the cDNA level, p.Thr106Ala (T106A) at the protein level, and results in the change of a Threonine to an Alanine (ACC>GCC). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. CDH1 Thr106Ala was not observed in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016). Since Threonine and Alanine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDH1 Thr106Ala occurs at a position that is not conserved and is located in the Precursor Sequence Domain (Brooks-Wilson 2004). In silico analyses predict that this variant is unlikely to alter protein structure or function. Based on currently available evidence, it is unclear whether CDH1 Thr106Ala is a pathogenic or benign variant. 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: May 1, 2024