NM_017799.4(TMEM260):c.344G>A (p.Arg115Lys) AND Structural heart defects and renal anomalies syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 5, 2021
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:: RCV001775195.1

Allele description [Variation Report for NM_017799.4(TMEM260):c.344G>A (p.Arg115Lys)]

NM_017799.4(TMEM260):c.344G>A (p.Arg115Lys)

Gene:

TMEM260:transmembrane protein 260 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q22.3

Genomic location:

Preferred name:

NM_017799.4(TMEM260):c.344G>A (p.Arg115Lys)

HGVS:

NC_000014.9:g.56585912G>A
NM_017799.4:c.344G>AMANE SELECT
NP_060269.3:p.Arg115Lys
NC_000014.8:g.57052630G>A

Protein change:

R115K; ARG115LYS

Links:

OMIM: 617449.0003; dbSNP: rs747632686

NCBI 1000 Genomes Browser:

rs747632686

Molecular consequence:

NM_017799.4:c.344G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Structural heart defects and renal anomalies syndrome (SHDRA)
Identifiers:: MONDO: MONDO:0044321; MedGen: C4479549; OMIM: 617478

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002011849	OMIM	no assertion criteria provided	Pathogenic (Nov 5, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002011849

OMIM

no assertion criteria provided

Pathogenic
(Nov 5, 2021)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects.

Pagnamenta AT, Jackson A, Perveen R, Beaman G, Petts G, Gupta A, Hyder Z, Chung BH, Kan AS, Cheung KW, Kerstjens-Frederikse WS, Abbott KM; Genomics England Research Consortium., Elpeleg O, Taylor JC, Banka S, Ta-Shma A.

Clin Genet. 2022 Jan;101(1):127-133. doi: 10.1111/cge.14071. Epub 2021 Oct 11.

PubMed [citation]

PMID:: 34612517

Details of each submission

From OMIM, SCV002011849.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a female and male fetus of British origin (family 1) with structural heart defects and renal anomalies syndrome (SHDRA; 617478), Pagnamenta et al. (2021) identified compound heterozygosity for mutations in the TMEM260 gene: a paternally inherited c.344G-A transition (c.344G-A, NM_017799.4), resulting in an arg115-to-lys (R115K) substitution, and a maternally inherited deletion (c.161_344del; 617449.0004) encompassing exons 2 and 3 and causing a frameshift predicted to result in a premature termination codon (Glu55PhefsTer20). The R115K variant was present at low frequency in the gnomAD database (2/249,706; v.2.1.1), whereas the exon 2-3 deletion was not found in gnomAD.

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

Last Updated: Dec 24, 2023

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