NM_001080517.3(SETD5):c.3253G>T (p.Gly1085Trp) AND Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency

Germline classification:: Uncertain significance (1 submission)
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:: RCV003339873.2

Allele description [Variation Report for NM_001080517.3(SETD5):c.3253G>T (p.Gly1085Trp)]

NM_001080517.3(SETD5):c.3253G>T (p.Gly1085Trp)

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.3253G>T (p.Gly1085Trp)

HGVS:

NC_000003.12:g.9473293G>T
NG_034132.1:g.80594G>T
NM_001080517.3:c.3253G>TMANE SELECT
NM_001292043.2:c.2959G>T
NM_001349451.2:c.2959G>T
NP_001073986.1:p.Gly1085Trp
NP_001278972.1:p.Gly987Trp
NP_001336380.1:p.Gly987Trp
NC_000003.11:g.9514977G>T

Protein change:

G1085W

Links:

dbSNP: rs767095342

NCBI 1000 Genomes Browser:

rs767095342

Molecular consequence:

NM_001080517.3:c.3253G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001292043.2:c.2959G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001349451.2:c.2959G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047800	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004047800

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004047800.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The c.3253G>T (p.Gly1085Trp) missense variant in SETD5 gene has been submitted to ClinVar as a Variant of Uncertain Significance. It has not been reported in affected individuals. This variant is reported with the allele frequency (0.0008%) in the gnomAD and novel in 1000 genome database. The amino acid Gly at position 1085 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Gly1085Trp in SETD5 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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