NM_205861.3(DHDDS):c.110G>A (p.Arg37His) AND Retinitis pigmentosa 59

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 7, 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:: RCV001858011.5

Allele description [Variation Report for NM_205861.3(DHDDS):c.110G>A (p.Arg37His)]

NM_205861.3(DHDDS):c.110G>A (p.Arg37His)

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.110G>A (p.Arg37His)

HGVS:

NC_000001.11:g.26438214G>A
NG_029786.1:g.10933G>A
NM_001243564.2:c.110G>A
NM_001243565.2:c.110G>A
NM_001319959.2:c.-193G>A
NM_024887.4:c.110G>A
NM_205861.3:c.110G>AMANE SELECT
NP_001230493.1:p.Arg37His
NP_001230494.1:p.Arg37His
NP_079163.2:p.Arg37His
NP_079163.2:p.Arg37His
NP_995583.1:p.Arg37His
NC_000001.10:g.26764705G>A
NM_024887.3:c.110G>A

Protein change:

R37H; ARG37HIS

Links:

OMIM: 608172.0002; dbSNP: rs1553121073

NCBI 1000 Genomes Browser:

rs1553121073

Molecular consequence:

NM_001319959.2:c.-193G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001243564.2:c.110G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243565.2:c.110G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024887.4:c.110G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_205861.3:c.110G>A - 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
SCV002216078	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 7, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 29100083, 31780880, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002216078

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 7, 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

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

Hamdan FF, Myers CT, Cossette P, Lemay P, Spiegelman D, Laporte AD, Nassif C, Diallo O, Monlong J, Cadieux-Dion M, Dobrzeniecka S, Meloche C, Retterer K, Cho MT, Rosenfeld JA, Bi W, Massicotte C, Miguet M, Brunga L, Regan BM, Mo K, Tam C, et al.

Am J Hum Genet. 2017 Nov 2;101(5):664-685. doi: 10.1016/j.ajhg.2017.09.008.

PubMed [citation]

PMID:: 29100083
PMCID:: PMC5673604

Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients.

Fernández-Marmiesse A, Roca I, Díaz-Flores F, Cantarín V, Pérez-Poyato MS, Fontalba A, Laranjeira F, Quintans S, Moldovan O, Felgueroso B, Rodríguez-Pedreira M, Simón R, Camacho A, Quijada P, Ibanez-Mico S, Domingno MR, Benito C, Calvo R, Pérez-Cejas A, Carrasco ML, Ramos F, Couce ML, et al.

Front Neurosci. 2019;13:1135. doi: 10.3389/fnins.2019.01135.

PubMed [citation]

PMID:: 31780880
PMCID:: PMC6856296

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002216078.3

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

Description

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 451635). This missense change has been observed in individual(s) with autosomal dominant developmental and epileptic encephalopathy (PMID: 29100083, 31780880). In at least one individual the variant was observed to be de novo. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 37 of the DHDDS protein (p.Arg37His).

#	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: Feb 14, 2024

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