NM_003000.3(SDHB):c.304G>A (p.Ala102Thr) AND Mitochondrial complex 2 deficiency, nuclear type 4

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Feb 1, 2013
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:: RCV001310281.7

Allele description [Variation Report for NM_003000.3(SDHB):c.304G>A (p.Ala102Thr)]

NM_003000.3(SDHB):c.304G>A (p.Ala102Thr)

Gene:

SDHB:succinate dehydrogenase complex iron sulfur subunit B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_003000.3(SDHB):c.304G>A (p.Ala102Thr)

HGVS:

NC_000001.11:g.17028719C>T
NG_012340.1:g.30452G>A
NM_003000.3:c.304G>AMANE SELECT
NP_002991.2:p.Ala102Thr
LRG_316t1:c.304G>A
LRG_316:g.30452G>A
NC_000001.10:g.17355214C>T
NC_000001.10:g.17355214C>T
NM_003000.2:c.304G>A

Protein change:

A102T; ALA102THR

Links:

OMIM: 185470.0024; dbSNP: rs777578399

NCBI 1000 Genomes Browser:

rs777578399

Molecular consequence:

NM_003000.3:c.304G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Mitochondrial complex 2 deficiency, nuclear type 4
Synonyms:: MITOCHONDRIAL COMPLEX II DEFICIENCY, NUCLEAR TYPE 4
Identifiers:: MONDO: MONDO:0030974; MedGen: C5543176; OMIM: 619224

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002564611	Arcensus	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 1, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002564611

Arcensus

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 1, 2013)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Novel variant p.(Ala102Thr) in SDHB causes mitochondrial complex II deficiency: Case report and review of the literature.

Kaur P, Sharma S, Kadavigere R, Girisha KM, Shukla A.

Ann Hum Genet. 2020 Jul;84(4):345-351. doi: 10.1111/ahg.12377. Epub 2020 Mar 2. Review.

PubMed [citation]

PMID:: 32124427

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV001500014.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In an Indian boy with mitochondrial complex II deficiency nuclear type 4 (MC2DN4; 619224), Kaur et al. (2020) identified a homozygous c.304G-A transition (c.304G-A, NM_003000.2) in the SDHB gene, resulting in an ala102-to-thr (A102T) substitution at a highly conserved residue. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in heterozygous state in the parents. The mutation was not present in homozygous state in the gnomAD database or in an in-house database of 569 individuals. In silico protein modeling suggested that the A102T substitution caused a gain of a polar contact in the SDHB protein, thus altering protein structure.

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

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053956.1

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

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

From Arcensus, SCV002564611.1

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

#	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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001500014	OMIM	flagged submission Reason: Claim with insufficient supporting evidence Notes: None	Pathogenic (Mar 8, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002053956	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	flagged submission Reason: Claim with insufficient supporting evidence Notes: None (ACMG Guidelines, 2015)	Likely pathogenic	inherited	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001500014

OMIM

flagged submission

Reason: Claim with insufficient supporting evidence

Notes: None

Pathogenic
(Mar 8, 2021)

germline

literature only

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

SCV002053956

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

flagged submission

Reason: Claim with insufficient supporting evidence

Notes: None

(ACMG Guidelines, 2015)

Likely pathogenic

inherited

research

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

Last Updated: Sep 29, 2024

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