NM_003002.4(SDHD):c.320T>G (p.Leu107Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 1, 2023
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:: RCV000219575.13

Allele description [Variation Report for NM_003002.4(SDHD):c.320T>G (p.Leu107Arg)]

NM_003002.4(SDHD):c.320T>G (p.Leu107Arg)

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.320T>G (p.Leu107Arg)

HGVS:

NC_000011.10:g.112094810T>G
NG_012337.3:g.12964T>G
NM_001276503.2:c.175T>G
NM_001276504.2:c.203T>G
NM_001276506.2:c.*18T>G
NM_003002.4:c.320T>GMANE SELECT
NP_001263432.1:p.Leu59Val
NP_001263433.1:p.Leu68Arg
NP_002993.1:p.Leu107Arg
LRG_9t1:c.320T>G
LRG_9:g.12964T>G
LRG_9p1:p.Leu107Arg
NC_000011.9:g.111965534T>G
NM_003002.2:c.320T>G
NM_003002.3:c.320T>G
NR_077060.2:n.409T>G

Protein change:

L107R

Links:

dbSNP: rs876658477

NCBI 1000 Genomes Browser:

rs876658477

Molecular consequence:

NM_001276506.2:c.*18T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276503.2:c.175T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276504.2:c.203T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003002.4:c.320T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_077060.2:n.409T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000273754	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Aug 1, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000273754

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Aug 1, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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

Tumor-specific prognosis of mutation-positive patients with head and neck paragangliomas.

Sen I, Young WF Jr, Kasperbauer JL, Polonis K, Harmsen WS, Colglazier JJ, DeMartino RR, Oderich GS, Kalra M, Bower TC.

J Vasc Surg. 2020 May;71(5):1602-1612.e2. doi: 10.1016/j.jvs.2019.08.232. Epub 2020 Feb 5.

PubMed [citation]

PMID:: 32035780

Details of each submission

From Ambry Genetics, SCV000273754.8

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

Description

The p.L107R variant (also known as c.320T>G), located in coding exon 4 of the SDHD gene, results from a T to G substitution at nucleotide position 320. The leucine at codon 107 is replaced by arginine, an amino acid with dissimilar properties. This alteration has been observed in multiple individuals who have a personal or family history that is consistent with SDHD-associated disease (Ambry internal data; Sen I et al. J Vasc Surg. 2020 05;71:1602-1612.e2). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

#	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: Oct 26, 2024

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