NM_003001.5(SDHC):c.387G>A (p.Trp129Ter) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 22, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000986019.6

Allele description [Variation Report for NM_003001.5(SDHC):c.387G>A (p.Trp129Ter)]

NM_003001.5(SDHC):c.387G>A (p.Trp129Ter)

Gene:

SDHC:succinate dehydrogenase complex subunit C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.3

Genomic location:

Preferred name:

NM_003001.5(SDHC):c.387G>A (p.Trp129Ter)

HGVS:

NC_000001.11:g.161356822G>A
NG_012767.1:g.47447G>A
NM_001035511.3:c.242-5507G>A
NM_001035512.3:c.285G>A
NM_001035513.3:c.228G>A
NM_001278172.3:c.140-5507G>A
NM_001407115.1:c.507G>A
NM_001407116.1:c.330G>A
NM_001407117.1:c.324G>A
NM_001407118.1:c.279G>A
NM_001407119.1:c.276G>A
NM_001407120.1:c.276G>A
NM_001407121.1:c.185-5507G>A
NM_003001.5:c.387G>AMANE SELECT
NP_001030589.1:p.Trp95Ter
NP_001030590.1:p.Trp76Ter
NP_001394044.1:p.Trp169Ter
NP_001394045.1:p.Trp110Ter
NP_001394046.1:p.Trp108Ter
NP_001394047.1:p.Trp93Ter
NP_001394048.1:p.Trp92Ter
NP_001394049.1:p.Trp92Ter
NP_002992.1:p.Trp129Ter
NP_002992.1:p.Trp129Ter
LRG_317t1:c.387G>A
LRG_317:g.47447G>A
LRG_317p1:p.Trp129Ter
NC_000001.10:g.161326612G>A
NM_003001.3:c.387G>A
NR_103459.3:n.439G>A

Protein change:

W108*

Links:

dbSNP: rs981049067

NCBI 1000 Genomes Browser:

rs981049067

Molecular consequence:

NM_001035511.3:c.242-5507G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001278172.3:c.140-5507G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407121.1:c.185-5507G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_103459.3:n.439G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001035512.3:c.285G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001035513.3:c.228G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407115.1:c.507G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407116.1:c.330G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407117.1:c.324G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407118.1:c.279G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407119.1:c.276G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407120.1:c.276G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_003001.5:c.387G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001134814	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Nov 2, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001765371	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 22, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001134814

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Nov 2, 2018)

germline

clinical testing

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

SCV001765371

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 22, 2020)

germline

clinical testing

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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001134814.2

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

Description

The variant creates a premature nonsense codon, and is therefore predicted to significantly disrupt the protein structure. Not found in the total gnomAD dataset, and the data is high quality.

#	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

From GeneDx, SCV001765371.1

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

Description

Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 41 amino acids are lost, and other loss-of-function variants have been reported downstream in ClinVar (Landrum 2016); Not observed in large population cohorts (Lek 2016); Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Sep 29, 2024

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