VCV002638524.12 - ClinVar

NM_205861.3(DHDDS):c.191G>A (p.Trp64Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_205861.3(DHDDS):c.191G>A (p.Trp64Ter)

Variation ID: 2638524 Accession: VCV002638524.12

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p36.11 1: 26442741 (GRCh38) [ NCBI UCSC ] 1: 26769232 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 20, 2023	Dec 22, 2024	May 30, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_205861.3:c.191G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_995583.1:p.Trp64Ter	nonsense
NM_001243564.2:c.191G>A	NP_001230493.1:p.Trp64Ter	nonsense
NM_001243565.2:c.191G>A	NP_001230494.1:p.Trp64Ter	nonsense
NM_001319959.2:c.-89G>A		5 prime UTR
NM_024887.4:c.191G>A	NP_079163.2:p.Trp64Ter	nonsense
NC_000001.11:g.26442741G>A
NC_000001.10:g.26769232G>A
NG_029786.1:g.15460G>A

... more HGVS ... less HGVS

Protein change

W64*

Other names

Canonical SPDI

NC_000001.11:26442740:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA339140082 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DHDDS		-	-	GRCh38 GRCh37	556	565

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (1)	criteria provided, single submitter	Mar 1, 2022	RCV003412947.11
Retinitis pigmentosa 59	Pathogenic (1)	criteria provided, single submitter	May 30, 2023	RCV003525406.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (May 30, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Retinitis pigmentosa 59 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004312459.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Publications: PubMed (2) PubMed: 27343064‚ 24664742 Comment: This premature translational stop signal has been observed in individual(s) with congenital disorders of glycosylation (PMID: 27343064). For these reasons, this variant has been classified … (more) This premature translational stop signal has been observed in individual(s) with congenital disorders of glycosylation (PMID: 27343064). For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp64*) in the DHDDS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DHDDS are known to be pathogenic (PMID: 24664742). (less)
Uncertain significance (Mar 01, 2022)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004123567.11 First in ClinVar: Nov 20, 2023 Last updated: Dec 22, 2024	Comment: DHDDS: PM2 Number of individuals with the variant: 1

Comment:

This premature translational stop signal has been observed in individual(s) with congenital disorders of glycosylation (PMID: 27343064). For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp64*) in the DHDDS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DHDDS are known to be pathogenic (PMID: 24664742).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
A case of fatal Type I congenital disorders of glycosylation (CDG I) associated with low dehydrodolichol diphosphate synthase (DHDDS) activity.	Sabry S	Orphanet journal of rare diseases	2016	PMID: 27343064
Knock-down DHDDS expression induces photoreceptor degeneration in zebrafish.	Wen R	Advances in experimental medicine and biology	2014	PMID: 24664742

Text-mined citations for this variant ...

Record last updated Dec 22, 2024

ClinVar Genomic variation as it relates to human health

NM_205861.3(DHDDS):c.191G>A (p.Trp64Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...