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NM_005390.5(PDHA2):c.679A>G (p.Met227Val) AND Spermatogenic failure 70

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 6, 2022
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV002221240.1

Allele description [Variation Report for NM_005390.5(PDHA2):c.679A>G (p.Met227Val)]

NM_005390.5(PDHA2):c.679A>G (p.Met227Val)

Gene:
PDHA2:pyruvate dehydrogenase E1 subunit alpha 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q22.3
Genomic location:
Preferred name:
NM_005390.5(PDHA2):c.679A>G (p.Met227Val)
Other names:
rs200969445; PDHA2, MET227VAL (rs200969445)
HGVS:
  • NC_000004.12:g.95840829A>G
  • NM_005390.5:c.679A>GMANE SELECT
  • NP_005381.1:p.Met227Val
  • NC_000004.11:g.96761980A>G
  • NM_005390.1:c.679A>G
Protein change:
M227V; MET227VAL
Links:
OMIM: 179061.0001; dbSNP: rs200969445
NCBI 1000 Genomes Browser:
rs200969445
Molecular consequence:
  • NM_005390.5:c.679A>G - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
effect on protein activity [Variation Ontology: 0053]

Condition(s)

Name:
Spermatogenic failure 70
Identifiers:
MONDO: MONDO:0030733; MedGen: C5676962; OMIM: 619828

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002498699OMIM
no assertion criteria provided
Pathogenic
(Apr 6, 2022)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Linked homozygous BMPR1B and PDHA2 variants in a consanguineous family with complex digit malformation and male infertility.

Yıldırım Y, Ouriachi T, Woehlbier U, Ouahioune W, Balkan M, Malik S, Tolun A.

Eur J Hum Genet. 2018 Jun;26(6):876-885. doi: 10.1038/s41431-018-0121-7. Epub 2018 Mar 26.

PubMed [citation]
PMID:
29581481
PMCID:
PMC5973948

Whole-exome sequencing improves the diagnosis and care of men with non-obstructive azoospermia.

Kherraf ZE, Cazin C, Bouker A, Fourati Ben Mustapha S, Hennebicq S, Septier A, Coutton C, Raymond L, Nouchy M, Thierry-Mieg N, Zouari R, Arnoult C, Ray PF.

Am J Hum Genet. 2022 Mar 3;109(3):508-517. doi: 10.1016/j.ajhg.2022.01.011. Epub 2022 Feb 15.

PubMed [citation]
PMID:
35172124
PMCID:
PMC8948161

Details of each submission

From OMIM, SCV002498699.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 3 infertile brothers from a consanguineous Algerian family with azoospermia (patients 406 and 412) or severe oligoasthenospermia (patient 401) (SPGF70; 619828), Yildirim et al. (2018) identified homozygosity for a c.679A-G transition (c.679A-G, NM_005390.1) in the PDHA2 gene, resulting in a met227-to-val (M227V) substitution at a highly conserved residue. Sanger sequencing confirmed the mutation and segregation with disease in the family; a heterozygous brother (409) showed mild necrozoospermia on semen analysis but was fertile. Female fertility appeared to be unaffected: a homozygous unmarried sister (408) had normal gonadotropic hormone levels. The mutation was present in the ExAC database at a low minor allele frequency (0.00009 in the Latino population and .00006 in the non-Finnish European population). Seven of 10 sibs in the family, including the 3 infertile brothers, also exhibited digital anomalies that were attributed to a linked mutation in the BMPR1B gene (see 603248).

In 2 unrelated infertile Tunisian men (P0253 and P0144) with azoospermia, Kherraf et al. (2022) identified homozygosity for the previously reported M227V substitution in the PDHA2 gene. Familial segregation was not reported; the variant was present in the gnomAD database at low minor allele frequency (.00006). The authors noted that although both men were homozygous for the same mutation, they exhibited different histologic subphenotypes and different outcomes on testicular sperm extraction (TESE), with one (P0253) showing hypospermatogenesis and a positive TESE, and the other (P0144) showing meiotic arrest and a negative TESE.

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

Last Updated: Dec 24, 2023