NM_004287.5(GOSR2):c.7C>A (p.Pro3Thr) AND not specified

Germline classification:: Benign (4 submissions)
Last evaluated:: Jul 3, 2017
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:: RCV000173332.17

Allele description [Variation Report for NM_004287.5(GOSR2):c.7C>A (p.Pro3Thr)]

NM_004287.5(GOSR2):c.7C>A (p.Pro3Thr)

Genes:

GOSR2:golgi SNAP receptor complex member 2 [Gene - OMIM - HGNC]
LRRC37A2:leucine rich repeat containing 37 member A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.32

Genomic location:

Preferred name:

NM_004287.5(GOSR2):c.7C>A (p.Pro3Thr)

Other names:

p.P3T:CCC>ACC

HGVS:

NC_000017.11:g.46923199C>A
NG_031806.2:g.5080C>A
NM_001012511.3:c.7C>A
NM_001321133.2:c.7C>A
NM_001321134.2:c.-96C>A
NM_001330252.2:c.7C>A
NM_001353114.2:c.7C>A
NM_001353115.2:c.7C>A
NM_001353116.2:c.7C>A
NM_001363851.2:c.-459C>A
NM_004287.5:c.7C>AMANE SELECT
NM_004287.5:c.7C>A
NM_054022.4:c.7C>A
NP_001012529.1:p.Pro3Thr
NP_001308062.1:p.Pro3Thr
NP_001317181.1:p.Pro3Thr
NP_001340043.1:p.Pro3Thr
NP_001340044.1:p.Pro3Thr
NP_001340045.1:p.Pro3Thr
NP_004278.2:p.Pro3Thr
NP_004278.2:p.Pro3Thr
NP_473363.1:p.Pro3Thr
NC_000017.10:g.45000565C>A
NM_004287.3:c.7C>A
NM_004287.4:c.7C>A
NM_054022.2:c.7C>A
NR_148349.2:n.40C>A
NR_148350.2:n.40C>A
NR_148351.2:n.40C>A

Protein change:

P3T

Links:

dbSNP: rs12944167

NCBI 1000 Genomes Browser:

rs12944167

Molecular consequence:

NM_001321134.2:c.-96C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001363851.2:c.-459C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001012511.3:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321133.2:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001330252.2:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353114.2:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353115.2:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353116.2:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004287.5:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_054022.4:c.7C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148349.2:n.40C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148350.2:n.40C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148351.2:n.40C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000168692	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Dec 1, 2013)	germline	clinical testing	Citation Link,
SCV000224432	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Jan 7, 2015)	germline	clinical testing	Citation Link,
SCV000310065	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000613538	Athena Diagnostics Inc	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jul 3, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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	3	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 GeneDx, SCV000168692.12

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Eurofins Ntd Llc (ga), SCV000224432.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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	unknown	not provided	not provided	not provided		3	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000310065.1

#	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 Athena Diagnostics Inc, SCV000613538.1

#	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: Apr 15, 2024

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