NM_004360.5(CDH1):c.393C>T (p.Ser131=) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: May 3, 2021
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:: RCV000679575.11

Allele description [Variation Report for NM_004360.5(CDH1):c.393C>T (p.Ser131=)]

NM_004360.5(CDH1):c.393C>T (p.Ser131=)

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.393C>T (p.Ser131=)

HGVS:

NC_000016.10:g.68808429C>T
NG_008021.1:g.76138C>T
NM_001317184.2:c.393C>T
NM_001317185.2:c.-1223C>T
NM_001317186.2:c.-1427C>T
NM_004360.5:c.393C>TMANE SELECT
NP_001304113.1:p.Ser131=
NP_004351.1:p.Ser131=
LRG_301t1:c.393C>T
LRG_301:g.76138C>T
NC_000016.9:g.68842332C>T
NM_004360.3:c.393C>T
NM_004360.4:c.393C>T
p.S131S

Links:

dbSNP: rs145430811

NCBI 1000 Genomes Browser:

rs145430811

Molecular consequence:

NM_001317185.2:c.-1223C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1427C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.393C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004360.5:c.393C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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myristoylated alanine-rich C-kinase substrate [Homo sapiens]
myristoylated alanine-rich C-kinase substrate [Homo sapiens]
gi|153070260|ref|NP_002347.5|

Protein
PLD4 [Crocodylus porosus]
PLD4 [Crocodylus porosus]
Gene ID:109320631

Gene
HAO1 [Tauraco erythrolophus]
HAO1 [Tauraco erythrolophus]
Gene ID:104383180

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000806669	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Dec 28, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001945445	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV002047265	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (May 3, 2021)	unknown	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

SCV000806669

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Dec 28, 2017)

germline

clinical testing

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

SCV001945445

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Mar 3, 2015)

germline

clinical testing

Citation Link,

SCV002047265

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Benign
(May 3, 2021)

unknown

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	unknown	unknown	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
not provided	germline	yes	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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV000806669.1

#	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

From GeneDx, SCV001945445.2

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

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002047265.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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