NM_004168.4(SDHA):c.1523C>T (p.Thr508Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 12, 2021
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:: RCV000563852.11

Allele description [Variation Report for NM_004168.4(SDHA):c.1523C>T (p.Thr508Ile)]

NM_004168.4(SDHA):c.1523C>T (p.Thr508Ile)

Gene:

SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_004168.4(SDHA):c.1523C>T (p.Thr508Ile)

Other names:

p.Thr508Ile

HGVS:

NC_000005.10:g.240448C>T
NG_012339.1:g.27208C>T
NM_001294332.2:c.1379C>T
NM_001330758.2:c.1523C>T
NM_004168.4:c.1523C>TMANE SELECT
NP_001281261.1:p.Thr460Ile
NP_001317687.1:p.Thr508Ile
NP_004159.2:p.Thr508Ile
LRG_315t1:c.1523C>T
LRG_315:g.27208C>T
LRG_315p1:p.Thr508Ile
NC_000005.9:g.240563C>T
NM_004168.2:c.1523C>T
NM_004168.3:c.1523C>T

Protein change:

T460I; THR508ILE

Links:

OMIM: 600857.0006; dbSNP: rs151266052

NCBI 1000 Genomes Browser:

rs151266052

Molecular consequence:

NM_001294332.2:c.1379C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001330758.2:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004168.4:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000664505	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jul 19, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002527718	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Jan 12, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000664505

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jul 19, 2018)

germline

clinical testing

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

Citation Link,

SCV002527718

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Benign
(Jan 12, 2021)

germline

curation

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, curation

Citations

PubMed

Recessive germline SDHA and SDHB mutations causing leukodystrophy and isolated mitochondrial complex II deficiency.

Alston CL, Davison JE, Meloni F, van der Westhuizen FH, He L, Hornig-Do HT, Peet AC, Gissen P, Goffrini P, Ferrero I, Wassmer E, McFarland R, Taylor RW.

J Med Genet. 2012 Sep;49(9):569-77. doi: 10.1136/jmedgenet-2012-101146.

PubMed [citation]

PMID:: 22972948
PMCID:: PMC3500770

Details of each submission

From Ambry Genetics, SCV000664505.5

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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 Sema4, Sema4, SCV002527718.1

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

#	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: Nov 3, 2024

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