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NM_003500.4(ACOX2):c.673C>T (p.Arg225Trp) AND Congenital bile acid synthesis defect 6

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
May 2, 2024
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:
RCV000417194.9

Allele description [Variation Report for NM_003500.4(ACOX2):c.673C>T (p.Arg225Trp)]

NM_003500.4(ACOX2):c.673C>T (p.Arg225Trp)

Gene:
ACOX2:acyl-CoA oxidase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p14.3
Genomic location:
Preferred name:
NM_003500.4(ACOX2):c.673C>T (p.Arg225Trp)
Other names:
ACOX2, ARG225TRP (rs150832314); c.673C>T; p.R225W
HGVS:
  • NC_000003.12:g.58531723G>A
  • NG_052668.1:g.10480C>T
  • NM_003500.4:c.673C>TMANE SELECT
  • NP_003491.1:p.Arg225Trp
  • NC_000003.11:g.58517450G>A
  • NM_003500.3:c.673C>T
Protein change:
R225W; ARG225TRP
Links:
OMIM: 601641.0002; dbSNP: rs150832314
NCBI 1000 Genomes Browser:
rs150832314
Molecular consequence:
  • NM_003500.4:c.673C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
Decreased function
Observations:
6

Condition(s)

Name:
Congenital bile acid synthesis defect 6
Identifiers:
MONDO: MONDO:0015015; MedGen: C4310624; OMIM: 617308

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000502996OMIM
no assertion criteria provided
Pathogenic
(Nov 15, 2023)
germlineliterature only

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

SCV002021278Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Dec 24, 2019)
germlineclinical testing

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

SCV004041815Valdecilla Biomedical Research Institute, Instituto de Salud Carlos III
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 11, 2023)
germline, not applicableclinical testing, in vitro

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

SCV005186014Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(May 2, 2024)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot applicablenot applicablenot providednot providednot providednot providednot providedin vitro
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
Caucasiangermlineyes54not providednot providednot providedclinical testing
Europeangermlineno72not 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

Beneficial effect of ursodeoxycholic acid in patients with acyl-CoA oxidase 2 (ACOX2) deficiency-associated hypertransaminasemia.

Alonso-Peña M, Espinosa-Escudero R, Herraez E, Briz O, Cagigal ML, Gonzalez-Santiago JM, Ortega-Alonso A, Fernandez-Rodriguez C, Bujanda L, Calvo Sanchez M, D Avola D, Londoño MC, Diago M, Fernandez-Checa JC, Garcia-Ruiz C, Andrade RJ, Lammert F, Prieto J, Crespo J, Juamperez J, Diaz-Gonzalez A, Monte MJ, et al.

Hepatology. 2022 Nov;76(5):1259-1274. doi: 10.1002/hep.32517. Epub 2022 Jul 1.

PubMed [citation]
PMID:
35395098
PMCID:
PMC9796151
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000502996.2

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

Description

In a brother and sister, born of parents from neighboring valleys in northern Spain, with congenital bile acid synthesis defect-6 (CBAS6; 617308), Monte et al. (2017) identified a homozygous c.673C-T transition (c.673C-T, NM_003500) in exon 6 of the ACOX2 gene, resulting in an arg225-to-trp (R225W) substitution. The mutation, which was found by direct sequencing of the gene, was present in heterozygous state in the unaffected parents. It was found at a low frequency (0.04%) in the dbSNP database. In vitro functional expression studies in human hepatoblastoma cells showed that the mutant protein was expressed at levels comparable to wildtype and localized properly to the peroxisome, but resulted in significantly decreased production of cholic acid compared to controls. Incubation of hepatoblastoma cells with THCA caused oxidative stress and cell death in a dose-dependent manner, which could be rescued by wildtype ACOX2, but not R225W ACOX2.

In 4 patients from 2 generations of a family (case 1) and an unrelated patient (case 2) with CBAS6, Alonso-Pena et al. (2022) identified homozygosity for the R225W mutation in the ACOX2 gene. The mutation was identified by sequencing of the ACOX2 gene and segregated with disease in the families. Liver biopsies from 2 of the patients demonstrated absence of ACOX2 expression.

In 2 unrelated patients (cases 3 and 4) with CBAS6, Alonso-Pena et al. (2022) identified compound heterozygous mutations in the ACOX2 gene: R225W and a 4-bp deletion (c.456_459del; 601641.0004) resulting in a frameshift and premature termination (Thr154fs). The mutation was identified by sequencing of the ACOX2 gene and segregated with disease in the families. Liver biopsies from the 2 patients demonstrated absence of ACOX2 expression. Both patients had accumulation of C27 bile acids.

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

From Revvity Omics, Revvity, SCV002021278.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Valdecilla Biomedical Research Institute, Instituto de Salud Carlos III, SCV004041815.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedin vitro PubMed (1)
2Caucasian5not providednot providedclinical testing PubMed (1)
3European2not providednot providedclinical testing PubMed (1)
4European5not providednot providedclinical testing PubMed (1)

Description

According to "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" (oi:10.1038/gim.2015.30), the variant should be classified as "likely pathogenic", as literature supports strong evidence of pathogenicity (PS3), Moderate evidence of pathogenicity (PM2, PM3) and Supporting evidence of pathogenicity (PP3).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not applicablenot applicablenot providednot providednot providednot providednot providednot providednot provided
2germlineyesnot providednot providednot provided5not provided4not provided
3germlinenonot providednot providednot provided2not provided2not provided
4germlinenonot providednot providednot provided5not provided4not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005186014.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: ACOX2 c.673C>T (p.Arg225Trp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00032 in 251358 control chromosomes. c.673C>T has been reported in the literature in multiple individuals affected with Congenital Bile Acid Synthesis Defect 6 (Alonso-Pena_2022, Monte_2017). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function and suggests an impact on protein function (Monte_2017). The following publications have been ascertained in the context of this evaluation (PMID: 27884763, 35395098). ClinVar contains an entry for this variant (Variation ID: 375691). Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Oct 13, 2024