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NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp) AND Rabin-Pappas syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 13, 2022
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV002467447.1

Allele description [Variation Report for NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp)]

NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp)

Gene:
SETD2:SET domain containing 2, histone lysine methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp)
HGVS:
  • NC_000003.12:g.47088172G>A
  • NG_032091.1:g.80806C>T
  • NM_001349370.3:c.5086C>T
  • NM_014159.7:c.5218C>TMANE SELECT
  • NP_001336299.1:p.Arg1696Trp
  • NP_054878.5:p.Arg1740Trp
  • NP_054878.5:p.Arg1740Trp
  • LRG_775t1:c.5218C>T
  • LRG_775:g.80806C>T
  • LRG_775p1:p.Arg1740Trp
  • NC_000003.11:g.47129662G>A
  • NM_014159.6:c.5218C>T
  • NR_146158.3:n.5407C>T
Protein change:
R1696W; ARG1740TRP
Links:
OMIM: 612778.0005; dbSNP: rs1057523157
NCBI 1000 Genomes Browser:
rs1057523157
Molecular consequence:
  • NM_001349370.3:c.5086C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014159.7:c.5218C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_146158.3:n.5407C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Rabin-Pappas syndrome
Identifiers:
MONDO: MONDO:0859331; MedGen: C5774269; OMIM: 620155

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002762854OMIM
no assertion criteria provided
Pathogenic
(Dec 13, 2022) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Genotype-phenotype correlation at codon 1740 of SETD2.

Rabin R, Radmanesh A, Glass IA, Dobyns WB, Aldinger KA, Shieh JT, Romoser S, Bombei H, Dowsett L, Trapane P, Bernat JA, Baker J, Mendelsohn NJ, Popp B, Siekmeyer M, Sorge I, Sansbury FH, Watts P, Foulds NC, Burton J, Hoganson G, Hurst JA, et al.

Am J Med Genet A. 2020 Sep;182(9):2037-2048. doi: 10.1002/ajmg.a.61724. Epub 2020 Jul 24.

PubMed [citation]
PMID:
32710489

Details of each submission

From OMIM, SCV002762854.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 12 unrelated patients (group 1) with Rabin-Pappas syndrome (RAPAS; 620155), Rabin et al. (2020) identified a de novo heterozygous c.5218C-T transition (c.5218C-T, NM_014159.6) in the SETD2 gene, resulting in an arg1740-to-trp (R1740W) substitution at conserved residue in a region of unknown function. The mutation, which was found through clinical genetics services, was not present in the gnomAD database. The patients were ascertained through collaborative efforts, and the phenotype determined retrospectively. Functional studies of the variant and studies of patient cells were not performed. The patients had a severe phenotype with intellectual disability, inability to walk or speak, and involvement of multiple organ systems, which was considered to be different from that of patients with other SETD2 mutations.

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

Last Updated: Nov 24, 2024