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NM_007373.4(SHOC2):c.566A>T (p.Tyr189Phe) AND RASopathy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 16, 2019
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:
RCV001030085.10

Allele description [Variation Report for NM_007373.4(SHOC2):c.566A>T (p.Tyr189Phe)]

NM_007373.4(SHOC2):c.566A>T (p.Tyr189Phe)

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.566A>T (p.Tyr189Phe)
HGVS:
  • NC_000010.11:g.110964924A>T
  • NG_028922.1:g.50382A>T
  • NM_001269039.3:c.566A>T
  • NM_001324336.2:c.566A>T
  • NM_001324337.2:c.566A>T
  • NM_007373.4:c.566A>TMANE SELECT
  • NP_001255968.1:p.Tyr189Phe
  • NP_001311265.1:p.Tyr189Phe
  • NP_001311266.1:p.Tyr189Phe
  • NP_031399.2:p.Tyr189Phe
  • NP_031399.2:p.Tyr189Phe
  • LRG_753t1:c.566A>T
  • LRG_753:g.50382A>T
  • LRG_753p1:p.Tyr189Phe
  • NC_000010.10:g.112724682A>T
  • NM_007373.3:c.566A>T
  • NR_136749.1:n.116-20704A>T
Protein change:
Y189F
Links:
dbSNP: rs1847644218
NCBI 1000 Genomes Browser:
rs1847644218
Molecular consequence:
  • NM_001269039.3:c.566A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324336.2:c.566A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324337.2:c.566A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007373.4:c.566A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001192877ClinGen RASopathy Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RASopathy ACMG Specifications v1)		Uncertain significance
(Sep 16, 2019) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen RASopathy Variant Curation Expert Panel, SCV001192877.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.556A>T (p.Tyr189Phe) variant in the SHOC2 gene is absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). The variant is located in the SHOC2 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, the clinical significance of the p.Tyr189Phe variant is uncertain. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM2, PP2.

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

Last Updated: Oct 20, 2024