NM_007373.4(SHOC2):c.1594A>G (p.Ser532Gly) AND RASopathy

Germline classification:: Benign (2 submissions)
Last evaluated:: Apr 18, 2017
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000476332.13

Allele description [Variation Report for NM_007373.4(SHOC2):c.1594A>G (p.Ser532Gly)]

NM_007373.4(SHOC2):c.1594A>G (p.Ser532Gly)

Gene:

SHOC2:SHOC2 leucine rich repeat scaffold protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q25.2

Genomic location:

Preferred name:

NM_007373.4(SHOC2):c.1594A>G (p.Ser532Gly)

Other names:

p.S532G:AGC>GGC; NM_007373.3(SHOC2):c.1594A>G

HGVS:

NC_000010.11:g.111011663A>G
NG_028922.1:g.97121A>G
NM_001269039.3:c.1456A>G
NM_001324336.2:c.1594A>G
NM_001324337.2:c.1594A>G
NM_007373.4:c.1594A>GMANE SELECT
NP_001255968.1:p.Ser486Gly
NP_001311265.1:p.Ser532Gly
NP_001311266.1:p.Ser532Gly
NP_031399.2:p.Ser532Gly
NP_031399.2:p.Ser532Gly
LRG_753t1:c.1594A>G
LRG_753:g.97121A>G
LRG_753p1:p.Ser532Gly
NC_000010.10:g.112771421A>G
NM_007373.3:c.1594A>G
NR_136749.2:n.945A>G

Protein change:

S486G

Links:

dbSNP: rs145463534

NCBI 1000 Genomes Browser:

rs145463534

Molecular consequence:

NM_001269039.3:c.1456A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001324336.2:c.1594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001324337.2:c.1594A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007373.4:c.1594A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136749.2:n.945A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: RASopathy
Synonyms:: rasopathies; Noonan spectrum disorder
Identifiers:: MONDO: MONDO:0021060; MedGen: C5555857

Recent activity

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Microbe sample from Streptococcus pluranimalium
Microbe sample from Streptococcus pluranimalium

biosample
Mus musculus 0 day neonate head cDNA, RIKEN full-length enriched library, clone:...
Mus musculus 0 day neonate head cDNA, RIKEN full-length enriched library, clone:4833419P04 product:hypothetical protein, full insert sequence
gi|26081305|dbj|AK029383.1|

Nucleotide
Homo sapiens chromosome 19 clone LLNLR-305D11, complete sequence
Homo sapiens chromosome 19 clone LLNLR-305D11, complete sequence
gi|12331458|gnl|lanlchgs|305D11|gb| 630.6|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000559052	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000616502	ClinGen RASopathy Variant Curation Expert Panel	reviewed by expert panel (ClinGen RASopathy ACMG Specifications v1)	Benign (Apr 18, 2017)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000559052

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

germline

clinical testing

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

SCV000616502

ClinGen RASopathy Variant Curation Expert Panel

reviewed by expert panel

(ClinGen RASopathy ACMG Specifications v1)

Benign
(Apr 18, 2017)

germline

curation

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000559052.9

#	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 ClinGen RASopathy Variant Curation Expert Panel, SCV000616502.4

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

Description

The filtering allele frequency of the c.1594A>G (p.Ser532Gly) variant in the SHOC2 gene is 1.147% (138/10402) of African chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)

#	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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