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NM_005334.3(HCFC1):c.218C>T (p.Ala73Val)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jul 1, 2020)
Last evaluated:
May 12, 2020
Accession:
VCV000066985.5
Variation ID:
66985
Description:
single nucleotide variant
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NM_005334.3(HCFC1):c.218C>T (p.Ala73Val)

Allele ID
77870
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153964702 (GRCh38) GRCh38 UCSC
X: 153230153 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153230153G>A
NC_000023.11:g.153964702G>A
NG_012513.1:g.11667C>T
NM_005334.3:c.218C>T MANE Select NP_005325.2:p.Ala73Val missense
Protein change
A73V
Other names
-
Canonical SPDI
NC_000023.11:153964701:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA144902
OMIM: 300019.0004
dbSNP: rs397515486
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Dec 23, 2015 RCV000224484.2
Pathogenic 1 criteria provided, single submitter Jul 25, 2014 RCV000224133.1
Pathogenic 1 criteria provided, single submitter May 12, 2020 RCV001199845.1
Pathogenic 1 no assertion criteria provided Sep 5, 2013 RCV000057507.17
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HCFC1 - - GRCh38
GRCh37
349 597

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 23, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281353.1
Submitted: (May 19, 2016)
Evidence details
Pathogenic
(Jul 25, 2014)
criteria provided, single submitter
Method: clinical testing
Intellectual disability
Allele origin: maternal
Diagnostic Laboratory, Strasbourg University Hospital
Accession: SCV000281741.1
Submitted: (Apr 20, 2015)
Evidence details
Comment:
present in the affected brother
Pathogenic
(May 12, 2020)
criteria provided, single submitter
Method: clinical testing
Methylmalonic acidemia with homocystinuria
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001370569.1
Submitted: (Jul 01, 2020)
Evidence details
Publications
PubMed (5)
Comment:
Variant summary: HCFC1 c.218C>T (p.Ala73Val) results in a non-conservative amino acid change located in the the first kelch domain (Yu_2013) of the encoded protein sequence. … (more)
Pathogenic
(Sep 05, 2013)
no assertion criteria provided
Method: literature only
METHYLMALONIC ACIDEMIA AND HOMOCYSTEINEMIA, cblX TYPE
Allele origin: germline
OMIM
Accession: SCV000088619.2
Submitted: (Oct 17, 2013)
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
Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias. Imperlini E BioMed research international 2016 PMID: 27403441
A novel <i>HCFC1</i> variant in male siblings with intellectual disability and microcephaly in the absence of cobalamin disorder. Koufaris C Biomedical reports 2016 PMID: 26893841
Hcfc1b, a zebrafish ortholog of HCFC1, regulates craniofacial development by modulating mmachc expression. Quintana AM Developmental biology 2014 PMID: 25281006
Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing. Redin C Journal of medical genetics 2014 PMID: 25167861
An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1. Yu HC American journal of human genetics 2013 PMID: 24011988

Text-mined citations for rs397515486...

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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 Nov 20, 2021