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NM_000191.3(HMGCL):c.914_915del (p.Phe305fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Nov 24, 2020)
Last evaluated:
Feb 3, 2020
Accession:
VCV000031084.4
Variation ID:
31084
Description:
2bp deletion
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NM_000191.3(HMGCL):c.914_915del (p.Phe305fs)

Allele ID
40041
Variant type
Deletion
Variant length
2 bp
Cytogenetic location
1p36.11
Genomic location
1: 23802526-23802527 (GRCh38) GRCh38 UCSC
1: 24129016-24129017 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.24129017_24129018del
NC_000001.11:g.23802527_23802528del
NM_000191.3:c.914_915del MANE Select NP_000182.2:p.Phe305fs frameshift
... more HGVS
Protein change
F305fs, F234fs
Other names
-
Canonical SPDI
NC_000001.11:23802525:AAA:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA261115
OMIM: 613898.0006
dbSNP: rs786205431
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Feb 3, 2020 RCV000032616.8
Pathogenic 1 criteria provided, single submitter Feb 20, 2015 RCV000724623.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HMGCL - - GRCh38
GRCh37
229 240

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jan 16, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of hydroxymethylglutaryl-CoA lyase
Allele origin: unknown
Counsyl
Accession: SCV000797207.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Feb 20, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232919.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Sep 24, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of hydroxymethylglutaryl-CoA lyase
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919524.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: HMGCL c.914_915delTT (p.Phe305TyrfsX10) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Feb 03, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of hydroxymethylglutaryl-CoA lyase
Allele origin: unknown
Centre for Mendelian Genomics,University Medical Centre Ljubljana
Accession: SCV001367088.2
Submitted: (Nov 24, 2020)
Evidence details
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2.
Pathogenic
(Feb 01, 1998)
no assertion criteria provided
Method: literature only
HMG-CoA LYASE DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000056376.3
Submitted: (Apr 14, 2011)
Evidence details
Publications
PubMed (1)

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
Ten novel HMGCL mutations in 24 patients of different origin with 3-hydroxy-3-methyl-glutaric aciduria. Menao S Human mutation 2009 PMID: 19177531
Mutations underlying 3-hydroxy-3-methylglutaryl CoA lyase deficiency in the Saudi population. Al-Sayed M BMC medical genetics 2006 PMID: 17173698
The E37X is a common HMGCL mutation in Portuguese patients with 3-hydroxy-3-methylglutaric CoA lyase deficiency. Cardoso ML Molecular genetics and metabolism 2004 PMID: 15308132
HMG CoA lyase deficiency: identification of five causal point mutations in codons 41 and 42, including a frequent Saudi Arabian mutation, R41Q. Mitchell GA American journal of human genetics 1998 PMID: 9463337
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HMGCL - - - -

Text-mined citations for rs786205431...

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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 Jun 14, 2021