chr10-117134019-C-CT

Variant names:

• chr10-117134019-C-CT
• rs1554942640
• NM_001112704.2:c.993dupA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001112704.2(VAX1):​c.993dupA​(p.Ala332SerfsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: VAX1 NM_001112704.2 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.556

Genes affected

VAX1 (HGNC:12660): (ventral anterior homeobox 1) This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors which are conserved in vertebrates. Genes of this family are involved in the regulation of body development and morphogenesis. The most conserved genes, called HOX genes are found in special gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play an important role in the development of anterior ventral forebrain and visual system. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VAX1	NM_001112704.2	c.993dupA	p.Ala332SerfsTer15	frameshift_variant	Exon 3 of 3	ENST00000369206.6	NP_001106175.1
VAX1	NM_199131.3	c.430-1543dupA		intron_variant	Intron 2 of 3		NP_954582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VAX1	ENST00000369206.6	c.993dupA	p.Ala332SerfsTer15	frameshift_variant	Exon 3 of 3	5	NM_001112704.2	ENSP00000358207.4
VAX1	ENST00000277905.6	c.430-1543dupA		intron_variant	Intron 2 of 3	1		ENSP00000277905.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1368944 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 674650

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Microphthalmia, syndromic 11 Uncertain:1

Apr 30, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change inserts 1 nucleotide in exon 3 of the VAX1 mRNA (c.993dupA), causing a frameshift at codon 332. It is expected to extend the length of the VAX1 protein by 11 amino acids. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a VAX1-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the additional amino acids is currently unknown. In summary, this variant is a novel stop-loss variant with uncertain impact on protein function. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1554942640; hg19: chr10-118893530;