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NM_000182.5(HADHA):c.1086-2A>T AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 6, 2021
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:
RCV001983859.2

Allele description [Variation Report for NM_000182.5(HADHA):c.1086-2A>T]

NM_000182.5(HADHA):c.1086-2A>T

Genes:
GAREM2:GRB2 associated regulator of MAPK1 subtype 2 [Gene - OMIM - HGNC]
HADHA:hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p23.3
Genomic location:
Preferred name:
NM_000182.5(HADHA):c.1086-2A>T
HGVS:
  • NC_000002.12:g.26204198T>A
  • NG_007121.2:g.45424A>T
  • NM_000182.5:c.1086-2A>TMANE SELECT
  • LRG_747t1:c.1086-2A>T
  • LRG_747:g.45424A>T
  • NC_000002.11:g.26427067T>A
Links:
dbSNP: rs2147762411
NCBI 1000 Genomes Browser:
rs2147762411
Molecular consequence:
  • NM_000182.5:c.1086-2A>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Mitochondrial trifunctional protein deficiency
Identifiers:
MONDO: MONDO:0012172; MedGen: C1969443; Orphanet: 746; OMIM: PS609015
Name:
Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency
Synonyms:
Deficiency of long-chain 3-hydroxyacyl-coenzyme A dehydrogenase; LCHAD Deficiency
Identifiers:
MONDO: MONDO:0012173; MedGen: C3711645; Orphanet: 5; OMIM: 609016

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002278400Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Sep 6, 2021) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Two alpha subunit donor splice site mutations cause human trifunctional protein deficiency.

Brackett JC, Sims HF, Rinaldo P, Shapiro S, Powell CK, Bennett MJ, Strauss AW.

J Clin Invest. 1995 May;95(5):2076-82.

PubMed [citation]
PMID:
7738175
PMCID:
PMC295799
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002278400.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant results in the deletion of part of exon 12 (c.1089-2_1089delins17) of the HADHA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in HADHA are known to be pathogenic (PMID: 7738175, 21103935, 21549624, 22459206). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with HADHA-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Sep 29, 2024