NM_004360.5(CDH1):c.199G>A (p.Ala67Thr) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 14, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000479101.10

Allele description [Variation Report for NM_004360.5(CDH1):c.199G>A (p.Ala67Thr)]

NM_004360.5(CDH1):c.199G>A (p.Ala67Thr)

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.199G>A (p.Ala67Thr)

HGVS:

NC_000016.10:g.68801705G>A
NG_008021.1:g.69414G>A
NM_001317184.2:c.199G>A
NM_001317185.2:c.-1417G>A
NM_001317186.2:c.-1621G>A
NM_004360.5:c.199G>AMANE SELECT
NP_001304113.1:p.Ala67Thr
NP_004351.1:p.Ala67Thr
LRG_301t1:c.199G>A
LRG_301:g.69414G>A
NC_000016.9:g.68835608G>A
NM_004360.3:c.199G>A
NM_004360.4:c.199G>A

Protein change:

A67T

Links:

dbSNP: rs1060501247

NCBI 1000 Genomes Browser:

rs1060501247

Molecular consequence:

NM_001317185.2:c.-1417G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1621G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.199G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.199G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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transcription elongation factor SPT6 isoform X1 [Homo sapiens]
transcription elongation factor SPT6 isoform X1 [Homo sapiens]
gi|2217313408|ref|XP_047292556.1|

Protein
OLR1 [Chlorocebus sabaeus]
OLR1 [Chlorocebus sabaeus]
Gene ID:103218575

Gene
HS3ST6 [Gracilinanus agilis]
HS3ST6 [Gracilinanus agilis]
Gene ID:123248629

Gene
Mixture/Component Compounds for PubChem Compound (Select 572) (23)
PubChem Compound
Taxonomy Links for Nucleotide (Select 1160688532) (1)
Taxonomy

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566211	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 14, 2023)	germline	clinical testing	Citation Link,
SCV000806652	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 24, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566211

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 14, 2023)

germline

clinical testing

Citation Link,

SCV000806652

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 24, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000566211.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 15235021)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000806652.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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