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NM_003002.4(SDHD):c.275A>T (p.Asp92Val) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 14, 2016
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:
RCV000479419.8

Allele description [Variation Report for NM_003002.4(SDHD):c.275A>T (p.Asp92Val)]

NM_003002.4(SDHD):c.275A>T (p.Asp92Val)

Gene:
SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.1
Genomic location:
Preferred name:
NM_003002.4(SDHD):c.275A>T (p.Asp92Val)
HGVS:
  • NC_000011.10:g.112088972A>T
  • NG_012337.3:g.7126A>T
  • NG_033145.1:g.2827T>A
  • NM_001276503.2:c.169+999A>T
  • NM_001276504.2:c.158A>T
  • NM_001276506.2:c.275A>T
  • NM_003002.4:c.275A>TMANE SELECT
  • NP_001263433.1:p.Asp53Val
  • NP_001263435.1:p.Asp92Val
  • NP_002993.1:p.Asp92Val
  • LRG_9t1:c.275A>T
  • LRG_9:g.7126A>T
  • LRG_9p1:p.Asp92Val
  • NC_000011.9:g.111959696A>T
  • NM_003002.2:c.275A>T
  • NM_003002.3:c.275A>T
  • NR_077060.2:n.310A>T
Protein change:
D53V
Links:
dbSNP: rs786205436
NCBI 1000 Genomes Browser:
rs786205436
Molecular consequence:
  • NM_001276503.2:c.169+999A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276504.2:c.158A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276506.2:c.275A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003002.4:c.275A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_077060.2:n.310A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000569592GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Apr 14, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000569592.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is denoted SDHD c.275A>T at the cDNA level, p.Asp92Val (D92V) at the protein level, and results in the change of an Aspartic Acid to a Valine (GAC>GTC). This variant has not, to our knowledge, been published in the literature as pathogenic or benign; however, another variant at the same residue, SDHD Asp92Tyr, is a well described Dutch pathogenic founder variant (van Schothorst 1998, Hensen 2010). SDHD Asp92Val was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Aspartic Acid and Valine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. SDHD Asp92Val occurs at a position that is conserved across species and is located in the transmembrane helical domain (UniProt). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on the currently available evidence, we consider SDHD Asp92Val to be a likely pathogenic variant.

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

Last Updated: May 26, 2024