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NM_145698.5(ACBD5):c.1467G>A (p.Trp489Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Aug 8, 2022
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:
RCV000760804.4

Allele description [Variation Report for NM_145698.5(ACBD5):c.1467G>A (p.Trp489Ter)]

NM_145698.5(ACBD5):c.1467G>A (p.Trp489Ter)

Gene:
ACBD5:acyl-CoA binding domain containing 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p12.1
Genomic location:
Preferred name:
NM_145698.5(ACBD5):c.1467G>A (p.Trp489Ter)
HGVS:
  • NC_000010.11:g.27204538C>T
  • NG_032960.3:g.49137G>A
  • NM_001042473.4:c.1362G>A
  • NM_001271512.3:c.1461G>A
  • NM_001301251.2:c.1140G>A
  • NM_001301252.2:c.1140G>A
  • NM_001301253.2:c.1140G>A
  • NM_001301254.2:c.936G>A
  • NM_001352568.1:c.1521G>A
  • NM_001352569.1:c.1500G>A
  • NM_001352570.1:c.1467G>A
  • NM_001352571.1:c.1494G>A
  • NM_001352572.1:c.1488G>A
  • NM_001352573.1:c.1446G>A
  • NM_001352574.2:c.1395G>A
  • NM_001352575.2:c.1395G>A
  • NM_001352576.2:c.1395G>A
  • NM_001352577.2:c.1362G>A
  • NM_001352578.2:c.1362G>A
  • NM_001352579.2:c.1362G>A
  • NM_001352580.2:c.1308G>A
  • NM_001352581.1:c.1296G>A
  • NM_001352582.2:c.1158G>A
  • NM_001352583.1:c.1140G>A
  • NM_001352584.1:c.1140G>A
  • NM_001352585.1:c.1173G>A
  • NM_001352586.1:c.1290G>A
  • NM_001352587.1:c.1257G>A
  • NM_001352588.1:c.1263G>A
  • NM_145698.5:c.1467G>AMANE SELECT
  • NP_001035938.1:p.Trp454Ter
  • NP_001258441.1:p.Trp487Ter
  • NP_001288180.1:p.Trp380Ter
  • NP_001288181.1:p.Trp380Ter
  • NP_001288182.1:p.Trp380Ter
  • NP_001288183.1:p.Trp312Ter
  • NP_001339497.1:p.Trp507Ter
  • NP_001339498.1:p.Trp500Ter
  • NP_001339499.1:p.Trp489Ter
  • NP_001339500.1:p.Trp498Ter
  • NP_001339501.1:p.Trp496Ter
  • NP_001339502.1:p.Trp482Ter
  • NP_001339503.1:p.Trp465Ter
  • NP_001339504.1:p.Trp465Ter
  • NP_001339505.1:p.Trp465Ter
  • NP_001339506.1:p.Trp454Ter
  • NP_001339507.1:p.Trp454Ter
  • NP_001339508.1:p.Trp454Ter
  • NP_001339509.1:p.Trp436Ter
  • NP_001339510.1:p.Trp432Ter
  • NP_001339511.1:p.Trp386Ter
  • NP_001339512.1:p.Trp380Ter
  • NP_001339513.1:p.Trp380Ter
  • NP_001339514.1:p.Trp391Ter
  • NP_001339515.1:p.Trp430Ter
  • NP_001339516.1:p.Trp419Ter
  • NP_001339517.1:p.Trp421Ter
  • NP_663736.2:p.Trp489Ter
  • NC_000010.10:g.27493467C>T
  • NM_145698.4:c.1467G>A
Protein change:
W312*
Links:
dbSNP: rs1564574359
NCBI 1000 Genomes Browser:
rs1564574359
Molecular consequence:
  • NM_001042473.4:c.1362G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001271512.3:c.1461G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301251.2:c.1140G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301252.2:c.1140G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301253.2:c.1140G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301254.2:c.936G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352568.1:c.1521G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352569.1:c.1500G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352570.1:c.1467G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352571.1:c.1494G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352572.1:c.1488G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352573.1:c.1446G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352574.2:c.1395G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352575.2:c.1395G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352576.2:c.1395G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352577.2:c.1362G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352578.2:c.1362G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352579.2:c.1362G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352580.2:c.1308G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352581.1:c.1296G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352582.2:c.1158G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352583.1:c.1140G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352584.1:c.1140G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352585.1:c.1173G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352586.1:c.1290G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352587.1:c.1257G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001352588.1:c.1263G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_145698.5:c.1467G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000890699GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Oct 19, 2018) 		germlineclinical testing

Citation Link,

SCV003314112Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 8, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes.

Abu-Safieh L, Alrashed M, Anazi S, Alkuraya H, Khan AO, Al-Owain M, Al-Zahrani J, Al-Abdi L, Hashem M, Al-Tarimi S, Sebai MA, Shamia A, Ray-Zack MD, Nassan M, Al-Hassnan ZN, Rahbeeni Z, Waheeb S, Alkharashi A, Abboud E, Al-Hazzaa SA, Alkuraya FS.

Genome Res. 2013 Feb;23(2):236-47. doi: 10.1101/gr.144105.112. Epub 2012 Oct 26.

PubMed [citation]
PMID:
23105016
PMCID:
PMC3561865

ACBD5 deficiency causes a defect in peroxisomal very long-chain fatty acid metabolism.

Ferdinandusse S, Falkenberg KD, Koster J, Mooyer PA, Jones R, van Roermund CWT, Pizzino A, Schrader M, Wanders RJA, Vanderver A, Waterham HR.

J Med Genet. 2017 May;54(5):330-337. doi: 10.1136/jmedgenet-2016-104132. Epub 2016 Oct 31.

PubMed [citation]
PMID:
27799409
See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000890699.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The W489X pathogenic variant in the ACBD5 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The W489X variant is not observed in large population cohorts (Lek et al., 2016). We interpret W489X as a pathogenic variant.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003314112.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Trp489*) in the ACBD5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ACBD5 are known to be pathogenic (PMID: 23105016, 27799409). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 620428). This premature translational stop signal has been observed in individual(s) with retinal dystrophy and leukodystrophy (PMID: 33427402). This variant is not present in population databases (gnomAD no frequency).

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

Last Updated: Sep 29, 2024