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NM_006662.3(SRCAP):c.7616C>T (p.Ser2539Leu) AND Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 20, 2023
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:
RCV004771659.1

Allele description [Variation Report for NM_006662.3(SRCAP):c.7616C>T (p.Ser2539Leu)]

NM_006662.3(SRCAP):c.7616C>T (p.Ser2539Leu)

Gene:
SRCAP:Snf2 related CREBBP activator protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p11.2
Genomic location:
Preferred name:
NM_006662.3(SRCAP):c.7616C>T (p.Ser2539Leu)
HGVS:
  • NC_000016.10:g.30737656C>T
  • NG_032135.1:g.43516C>T
  • NG_032135.2:g.43487C>T
  • NM_006662.3:c.7616C>TMANE SELECT
  • NP_006653.2:p.Ser2539Leu
  • NC_000016.9:g.30748977C>T
Protein change:
S2539L
Molecular consequence:
  • NM_006662.3:c.7616C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities
Identifiers:
MONDO: MONDO:0859202; MedGen: C5562012; OMIM: 619595

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005382316Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 20, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV005382316.1

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

Description

The observed missense variant c.7616C>T(p.Ser2539Leu) in SRCAP gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.7616C>T variant has 0.0004% allele frequency in gnomAD Exomes. The amino acid Serine at position 2539 is changed to a Leucine changing protein sequence and it might alter its composition and physico-chemical properties. Computational evidence (Polyphen, SIFT and Mutation Taster) predicts conflicting evidence on protein structure and function for this variant.The reference amino acid in SRCAP is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

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

Last Updated: Nov 3, 2024