NM_005522.5(HOXA1):c.175dup (p.Val59fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Apr 1, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001008325.1

Allele description [Variation Report for NM_005522.5(HOXA1):c.175dup (p.Val59fs)]

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

Gene:
HOXA1:homeobox A1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7p15.2
Genomic location:
Preferred name:
NM_005522.5(HOXA1):c.175dup (p.Val59fs)
HGVS:
  • NC_000007.14:g.27095743dup
  • NG_011813.1:g.5269dup
  • NG_033087.1:g.4650dup
  • NM_005522.4:c.175dup
  • NM_005522.5:c.175dupMANE SELECT
  • NM_153620.3:c.175dup
  • NP_005513.1:p.Val59fs
  • NP_005513.2:p.Val59fs
  • NP_705873.3:p.Val59fs
  • NC_000007.13:g.27135362dup
  • NM_005522.4:c.175dupG
Note:
ClinGen staff contributed the HGVS expression for this variant.
Protein change:
V59fs
Links:
OMIM: 142955.0001; dbSNP: rs769152039
NCBI 1000 Genomes Browser:
rs769152039
Molecular consequence:
  • NM_005522.4:c.175dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_005522.5:c.175dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_153620.3:c.175dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001168093GeneDxcriteria provided, single submitter
Pathogenic
(Apr 1, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168093.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 c.175dupG variant causes a frameshift starting with codon Valine 59, changes this amino acid to a Glycine residue, and creates a premature Stop codon at position 119 of the new reading frame, denoted p.Val59GlyfsX119. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.175dupG variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.175dupG as a pathogenic variant.

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

Last Updated: Nov 27, 2021

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