rs1553941938

chr4-42963095-T-TTCCC

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001080476.3(GRXCR1):c.594_597dup(p.Val200ProfsTer6) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GRXCR1 NM_001080476.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.67

Genes affected

GRXCR1 (HGNC:31673): (glutaredoxin and cysteine rich domain containing 1) This gene is one of 60 loci associated with autosomal-recessive nonsyndromic hearing impairment. This gene encodes a protein which contains GRX-like domains; these domains play a role in the S-glutathionylation of proteins and may be involved in actin organization in hair cells. [provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-42963095-T-TTCCC is Pathogenic according to our data. Variant chr4-42963095-T-TTCCC is described in ClinVar as [Pathogenic]. Clinvar id is 504921.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRXCR1	NM_001080476.3	c.594_597dup	p.Val200ProfsTer6	frameshift_variant	2/4	ENST00000399770.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRXCR1	ENST00000399770.3	c.594_597dup	p.Val200ProfsTer6	frameshift_variant	2/4	1	NM_001080476.3	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

May 01, 2016

The p.Val200fs variant in GRXCR1 has been identified in the homozygous state by our laboratory in 1 individual with hearing loss and segregated in an affected s ibling (this family). This variant was absent from large population studies, tho ugh the ability of these studies to accurately detect indels may be limited. The p.Val200fs variant is predicted to cause a frameshift, which alters the protein ?s amino acid sequence beginning at position 200 and leads to a premature termin ation codon 6 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function (LoF) variants in the GRXCR1 have been reported in individuals with hearing loss, and a mouse model study sup ports LoF as a disease mechanism (Odeh 2010). In summary, the p.Val200fs variant meets our criteria to be classified as pathogenic for hearing loss in an autoso mal recessive manner based on the predicted impact of the variant. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553941938; hg19: chr4-42965112;