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NM_002225.5(IVD):c.149G>C (p.Arg50Pro) AND IVD-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 31, 2024
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:
RCV003927565.2

Allele description [Variation Report for NM_002225.5(IVD):c.149G>C (p.Arg50Pro)]

NM_002225.5(IVD):c.149G>C (p.Arg50Pro)

Gene:
IVD:isovaleryl-CoA dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q15.1
Genomic location:
Preferred name:
NM_002225.5(IVD):c.149G>C (p.Arg50Pro)
HGVS:
  • NC_000015.10:g.40407640G>C
  • NG_011986.2:g.7156G>C
  • NM_001159508.3:c.145-299G>C
  • NM_001354597.3:c.101G>C
  • NM_001354598.3:c.149G>C
  • NM_001354599.3:c.149G>C
  • NM_001354600.3:c.149G>C
  • NM_001354601.3:c.149G>C
  • NM_002225.5:c.149G>CMANE SELECT
  • NP_001341526.1:p.Arg34Pro
  • NP_001341527.2:p.Arg50Pro
  • NP_001341528.2:p.Arg50Pro
  • NP_001341529.2:p.Arg50Pro
  • NP_001341530.2:p.Arg50Pro
  • NP_002216.3:p.Arg50Pro
  • NC_000015.9:g.40699841G>C
  • NM_002225.3:c.158G>C
  • NR_148925.2:n.561G>C
Protein change:
R34P
Links:
dbSNP: rs2229311
NCBI 1000 Genomes Browser:
rs2229311
Molecular consequence:
  • NM_001159508.3:c.145-299G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354597.3:c.101G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354598.3:c.149G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354599.3:c.149G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354600.3:c.149G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354601.3:c.149G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002225.5:c.149G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148925.2:n.561G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
IVD-related disorder
Synonyms:
IVD-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004740574PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 31, 2024)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 PreventionGenetics, part of Exact Sciences, SCV004740574.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The IVD c.158G>C variant is predicted to result in the amino acid substitution p.Arg53Pro. This variant, alternately described in the literature as Arg21Pro or c.149G>C, p.Arg50Pro, has been recurrently reported in patients with isovaleric acidemia and has been reported to impact protein function (Mohsen et al. 1998. PubMed ID: 9665741; Ensenauer et al. 2004. PubMed ID: 15486829; Sakamoto et al. 2015. PubMed ID: 26018748; Couce et al. 2016. PubMed ID: 27904153; D'Annibale et al. 2021. PubMed ID: 34535384; M├╝tze et al. 2021. PubMed ID: 33496032). Different substitutions of the same amino acid (p.Arg53Cys, p.Arg53His, p.Arg53Leu) have also been reported in isovaleric acidemia patients (Ensenauer et al. 2004. PubMed ID: 15486829; Lee et al. 2007. PubMed ID: 17576084; Li et al. 2019. PubMed ID: 31442447). This variant is reported in 0.0087% of alleles in individuals of Latino descent in gnomAD. This variant is interpreted as pathogenic.

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

Last Updated: Jun 23, 2024