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NM_000182.5(HADHA):c.1967del (p.Ile655_Leu656insTer)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 6, 2020)
Last evaluated:
Oct 21, 2019
Accession:
VCV000188712.3
Variation ID:
188712
Description:
1bp deletion
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NM_000182.5(HADHA):c.1967del (p.Ile655_Leu656insTer)

Allele ID
186665
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
2p23.3
Genomic location
2: 26192343 (GRCh38) GRCh38 UCSC
2: 26415212 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000182.4:c.1967del
LRG_747t1:c.1967del LRG_747p1:p.Ile655_Leu656insTer
NC_000002.11:g.26415215del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:26192342:AAAA:AAA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA199043
dbSNP: rs779113356
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts May 22, 2017 RCV000169001.2
Pathogenic 1 criteria provided, single submitter Aug 11, 2016 RCV000255407.1
Pathogenic 1 criteria provided, single submitter Oct 21, 2019 RCV001239627.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAREM2 - - GRCh38
GRCh37
1 257
HADHA - - GRCh38
GRCh37
217 476

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 04, 2014)
criteria provided, single submitter
Method: literature only
Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220140.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(May 22, 2017)
criteria provided, single submitter
Method: clinical testing
Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695944.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The HADHA c.1967delT (p.Leu656X) variant results in a premature termination codon, predicted to cause a truncated or absent HADHA protein due to nonsense … (more)
Pathogenic
(Aug 11, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000322387.7
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.1967delT has previously been reported as c.1964delT in association with LCHAD deficiency (Ibdah et al., 1999). This variant results in the normal codon, Leucine … (more)
Pathogenic
(Oct 21, 2019)
criteria provided, single submitter
Method: clinical testing
Mitochondrial trifunctional protein deficiency
Long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency
Allele origin: germline
Invitae
Accession: SCV001412513.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Leu656*) in the HADHA gene. It is expected to result in an absent or disrupted protein … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Comprehensive cDNA study and quantitative analysis of mutant HADHA and HADHB transcripts in a French cohort of 52 patients with mitochondrial trifunctional protein deficiency. Boutron A Molecular genetics and metabolism 2011 PMID: 21549624
A fetal fatty-acid oxidation disorder as a cause of liver disease in pregnant women. Ibdah JA The New England journal of medicine 1999 PMID: 10352164

Text-mined citations for rs779113356...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021