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NM_001080517.3(SETD5):c.3742C>T (p.Arg1248Trp) AND Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 25, 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:
RCV002471711.1

Allele description [Variation Report for NM_001080517.3(SETD5):c.3742C>T (p.Arg1248Trp)]

NM_001080517.3(SETD5):c.3742C>T (p.Arg1248Trp)

Gene:
SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_001080517.3(SETD5):c.3742C>T (p.Arg1248Trp)
HGVS:
  • NC_000003.12:g.9475504C>T
  • NG_034132.1:g.82805C>T
  • NM_001080517.1:c.3742C>T
  • NM_001080517.3:c.3742C>TMANE SELECT
  • NM_001292043.2:c.3448C>T
  • NM_001349451.2:c.3448C>T
  • NP_001073986.1:p.Arg1248Trp
  • NP_001278972.1:p.Arg1150Trp
  • NP_001336380.1:p.Arg1150Trp
  • NC_000003.11:g.9517188C>T
  • NM_001080517.2:c.3742C>T
Protein change:
R1150W
Molecular consequence:
  • NM_001080517.3:c.3742C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001292043.2:c.3448C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349451.2:c.3448C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency (MRD23)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 23
Identifiers:
MONDO: MONDO:0014336; MedGen: C3810406; Orphanet: 404440; OMIM: 615761

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002769197Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 25, 2020) 		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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769197.1

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

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from an arginine to a tryptophan (exon 23). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0309 - Two alternative amino acid changes at the same position to leucine (2 heterozygotes, 0 homozygotes) and glutamine (1 heterozygote, 0 homozygotes) have been observed in gnomAD. (N) 0502 - Missense variant with conflicting in-silico predictions and/or uninformative conservation. (N) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (N) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

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

Last Updated: Sep 29, 2024