NM_205861.3(DHDDS):c.292C>T (p.Arg98Trp) AND Retinitis pigmentosa 59

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 25, 2022
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:: RCV001862719.4

Allele description

NM_205861.3(DHDDS):c.292C>T (p.Arg98Trp)

Gene:

DHDDS:dehydrodolichyl diphosphate synthase subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.11

Genomic location:

Preferred name:

NM_205861.3(DHDDS):c.292C>T (p.Arg98Trp)

HGVS:

NC_000001.11:g.26442842C>T
NG_029786.1:g.15561C>T
NM_001243564.2:c.292C>T
NM_001243565.2:c.292C>T
NM_001319959.2:c.13C>T
NM_024887.4:c.292C>T
NM_205861.3:c.292C>TMANE SELECT
NP_001230493.1:p.Arg98Trp
NP_001230494.1:p.Arg98Trp
NP_001306888.1:p.Arg5Trp
NP_079163.2:p.Arg98Trp
NP_079163.2:p.Arg98Trp
NP_995583.1:p.Arg98Trp
NC_000001.10:g.26769333C>T
NC_000001.10:g.26769333C>T
NM_024887.3:c.292C>T

Protein change:

R5W

Links:

dbSNP: rs754564043

NCBI 1000 Genomes Browser:

rs754564043

Molecular consequence:

NM_001243564.2:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001243565.2:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001319959.2:c.13C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024887.4:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_205861.3:c.292C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Retinitis pigmentosa 59 (RP59)
Identifiers:: MONDO: MONDO:0013468; MedGen: C3151227; Orphanet: 791; OMIM: 613861

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002211922	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 25, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 29276052, 31456290, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002211922

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 25, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Nonsyndromic Retinitis Pigmentosa in the Ashkenazi Jewish Population: Genetic and Clinical Aspects.

Kimchi A, Khateb S, Wen R, Guan Z, Obolensky A, Beryozkin A, Kurtzman S, Blumenfeld A, Pras E, Jacobson SG, Ben-Yosef T, Newman H, Sharon D, Banin E.

Ophthalmology. 2018 May;125(5):725-734. doi: 10.1016/j.ophtha.2017.11.014. Epub 2017 Dec 22. Erratum in: Ophthalmology. 2020 Jan;127(1):139. doi: 10.1016/j.ophtha.2019.10.024.

PubMed [citation]

PMID:: 29276052

A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC).

Sharon D, Ben-Yosef T, Goldenberg-Cohen N, Pras E, Gradstein L, Soudry S, Mezer E, Zur D, Abbasi AH, Zeitz C, Cremers FPM, Khan MI, Levy J, Rotenstreich Y, Birk OS, Ehrenberg M, Leibu R, Newman H, Shomron N, Banin E, Perlman I.

Hum Mutat. 2020 Jan;41(1):140-149. doi: 10.1002/humu.23903. Epub 2019 Sep 15.

PubMed [citation]

PMID:: 31456290

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002211922.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 98 of the DHDDS protein (p.Arg98Trp). This variant is present in population databases (rs754564043, gnomAD 0.01%). This missense change has been observed in individual(s) with autosomal recessive retinitis pigmentosa (PMID: 29276052, 31456290). ClinVar contains an entry for this variant (Variation ID: 812306). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DHDDS protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Jun 23, 2024

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