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NM_001080517.3(SETD5):c.3006A>T (p.Gly1002=) AND Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 18, 2021
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:
RCV001723515.1

Allele description [Variation Report for NM_001080517.3(SETD5):c.3006A>T (p.Gly1002=)]

NM_001080517.3(SETD5):c.3006A>T (p.Gly1002=)

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.3006A>T (p.Gly1002=)
HGVS:
  • NC_000003.12:g.9470740A>T
  • NG_034132.1:g.78041A>T
  • NM_001080517.3:c.3006A>TMANE SELECT
  • NM_001292043.2:c.2712A>T
  • NM_001349451.2:c.2712A>T
  • NP_001073986.1:p.Gly1002=
  • NP_001278972.1:p.Gly904=
  • NP_001336380.1:p.Gly904=
  • NC_000003.11:g.9512424A>T
Links:
dbSNP: rs2125579215
NCBI 1000 Genomes Browser:
rs2125579215
Molecular consequence:
  • NM_001080517.3:c.3006A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001292043.2:c.2712A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001349451.2:c.2712A>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

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
SCV001950434Breda Genetics srl
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Feb 18, 2021) 		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 Breda Genetics srl, SCV001950434.1

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

Description

Based on allele frequency, in-silico prediction scores and a certain overlap with the clinical phenotype, we interpreted this variant at least as of uncertain significance. The lack of one or more of the following features has discouraged further investigations: lack of a possible second hit in autosomal recessive conditions, presence of healthy controls in databases for autosomal dominant conditions, presence of unmatching cardinal clinical features in the patient or in the known gene-disease association, and/or variant type outside the known gene mutational spectrum.

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

Last Updated: Dec 24, 2023