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NM_005522.5(HOXA1):c.175dup (p.Val59fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Oct 15, 2019)
Last evaluated:
Apr 1, 2019
Accession:
VCV000014898.5
Variation ID:
14898
Description:
1bp duplication
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NM_005522.5(HOXA1):c.175dup (p.Val59fs)

Allele ID
29937
Variant type
Duplication
Variant length
1 bp
Cytogenetic location
7p15.2
Genomic location
7: 27095737-27095738 (GRCh38) GRCh38 UCSC
7: 27135356-27135357 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_005522.4:c.175dup NP_005513.1:p.Val59fs frameshift
NM_005522.4:c.175dupG frameshift
NC_000007.13:g.27135362dup
... more HGVS
Protein change
V59fs
Other names
-
Canonical SPDI
NC_000007.14:27095737:CCCCCC:CCCCCCC
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
OMIM: 142955.0001
dbSNP: rs769152039
VarSome
Comment on variant
ClinGen staff contributed the HGVS expression for this variant.
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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 Apr 1, 2019 RCV001008325.1
Pathogenic 1 no assertion criteria provided May 15, 2008 RCV000016027.22
Pathogenic 1 no assertion criteria provided Jan 29, 2019 RCV000984930.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HOXA1 - - GRCh38
GRCh37
69 112

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Apr 01, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001168093.1
Submitted: (Oct 15, 2019)
Evidence details
Comment:
The c.175dupG variant in the HOXA1 gene has been reported previously as a homozygous variant in association with Bosley-Salih-Alorainy syndrome (Tischfield et al., 2005). The … (more)
Pathogenic
(May 15, 2008)
no assertion criteria provided
Method: literature only
BOSLEY-SALIH-ALORAINY SYNDROME
Allele origin: germline
OMIM
Accession: SCV000036294.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)
Pathogenic
(Jan 29, 2019)
no assertion criteria provided
Method: clinical testing
Human HOXA1 syndromes
Allele origin: germline
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City
Accession: SCV001132843.1
Submitted: (Sep 26, 2019)
Evidence details

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
The clinical spectrum of homozygous HOXA1 mutations. Bosley TM American journal of medical genetics. Part A 2008 PMID: 18412118
Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. Tischfield MA Nature genetics 2005 PMID: 16155570

Text-mined citations for rs769152039...

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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 24, 2021