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NM_001372044.2(SHANK3):c.1247C>T (p.Ser416Leu) AND Phelan-McDermid syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 24, 2024
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:
RCV004790115.1

Allele description [Variation Report for NM_001372044.2(SHANK3):c.1247C>T (p.Ser416Leu)]

NM_001372044.2(SHANK3):c.1247C>T (p.Ser416Leu)

Gene:
SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_001372044.2(SHANK3):c.1247C>T (p.Ser416Leu)
Other names:
p.Ser416Leu
HGVS:
  • NC_000022.11:g.50684643C>T
  • NG_070230.1:g.20371C>T
  • NM_001372044.2:c.1247C>TMANE SELECT
  • NP_001358973.1:p.Ser416Leu
  • NC_000022.10:g.51123071C>T
Protein change:
S416L
Molecular consequence:
  • NM_001372044.2:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Phelan-McDermid syndrome
Synonyms:
TELOMERIC 22q13 MONOSOMY SYNDROME; 22q13.3 deletion syndrome; Chromosome 22q13.3 deletion syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011652; MedGen: C1853490; Orphanet: 48652; OMIM: 606232

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005397919Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 24, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV005397919.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

A heterozygous missense variant in exon 11 of the SHANK3 gene that results in the amino acid substitution of Leucine for Serine at codon 416 was detected. The observed variant has not been reported in the 1000 genomes and gnomAD (v2.1) databases and has a minor allele frequency of 0.001%, 0.001% and 0.001% in the gnomAD (v3.1), topmed and in our internal databases respectively. The in-silico predictions of the variant is damaging by SIFT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 30, 2024