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NM_007373.4(SHOC2):c.610A>G (p.Ile204Val) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 7, 2020
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:
RCV001174950.1

Allele description [Variation Report for NM_007373.4(SHOC2):c.610A>G (p.Ile204Val)]

NM_007373.4(SHOC2):c.610A>G (p.Ile204Val)

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.610A>G (p.Ile204Val)
HGVS:
  • NC_000010.11:g.110964968A>G
  • NG_028922.1:g.50426A>G
  • NM_001269039.3:c.610A>G
  • NM_001324336.2:c.610A>G
  • NM_001324337.2:c.610A>G
  • NM_007373.4:c.610A>GMANE SELECT
  • NP_001255968.1:p.Ile204Val
  • NP_001311265.1:p.Ile204Val
  • NP_001311266.1:p.Ile204Val
  • NP_031399.2:p.Ile204Val
  • NP_031399.2:p.Ile204Val
  • LRG_753t1:c.610A>G
  • LRG_753:g.50426A>G
  • LRG_753p1:p.Ile204Val
  • NC_000010.10:g.112724726A>G
  • NM_007373.3:c.610A>G
Protein change:
I204V
Links:
dbSNP: rs200015085
NCBI 1000 Genomes Browser:
rs200015085
Molecular consequence:
  • NM_001269039.3:c.610A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324336.2:c.610A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324337.2:c.610A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007373.4:c.610A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001338411Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Feb 7, 2020) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Post-mortem whole-exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases.

Neubauer J, Lecca MR, Russo G, Bartsch C, Medeiros-Domingo A, Berger W, Haas C.

Eur J Hum Genet. 2017 Apr;25(4):404-409. doi: 10.1038/ejhg.2016.199. Epub 2017 Jan 11.

PubMed [citation]
PMID:
28074886
PMCID:
PMC5386419

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338411.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: SHOC2 c.610A>G (p.Ile204Val) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 6.8e-05 in 250862 control chromosomes (gnomAD). The observed variant frequency is approximately 2.7 fold the estimated maximal expected allele frequency for a pathogenic variant in SHOC2 causing Noonan Syndrome and Related Conditions phenotype (2.5e-05), strongly suggesting that the variant is benign. c.610A>G has been reported in the literature in an individual affected with SIDS (Naubauer_2017). This report does not provide unequivocal conclusions about association of the variant with Noonan Syndrome and Related Conditions. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, three classified the variant as VUS while one classified it as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024