rs58058996
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000424.4(KRT5):āc.482T>Gā(p.Ile161Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I161N) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000424.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT5 | NM_000424.4 | c.482T>G | p.Ile161Ser | missense_variant | 1/9 | ENST00000252242.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT5 | ENST00000252242.9 | c.482T>G | p.Ile161Ser | missense_variant | 1/9 | 1 | NM_000424.4 | P1 | |
KRT5 | ENST00000552629.5 | n.580T>G | non_coding_transcript_exon_variant | 1/7 | 1 | ||||
KRT5 | ENST00000549420.1 | c.152T>G | p.Ile51Ser | missense_variant | 2/5 | 5 | |||
KRT5 | ENST00000551275.1 | c.377T>G | p.Ile126Ser | missense_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2Other:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 03, 2021 | Located in the highly conserved head domain, preceding the helix initiation motif; keratin gene variants affecting the residues at the head domain in type II keratins are known to interfere with proper keratin intermediate filament assembly and function, resulting in skin fragility, blistering, and/or hyperkeratosis (Chamcheu et al., 2011); Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 7537780, 29334134, 7688477, 27065010, 16098032, 27535533) - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | This sequence change replaces isoleucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 161 of the KRT5 protein (p.Ile161Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant epidermolysis bullosa simplex (PMID: 7537780, 7688477, 16098032). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14640). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt KRT5 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. - |
not provided, no classification provided | literature only | Epithelial Biology; Institute of Medical Biology, Singapore | - | - - |
Epidermolysis bullosa simplex 2C, localized Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2005 | - - |
Epidermolysis bullosa simplex 1C, localized Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Jun 14, 2021 | PP1_strong, PS4, PM5_Supporting, PP3, PM1, PM2 - |
KRT5-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 19, 2023 | The KRT5 c.482T>G variant is predicted to result in the amino acid substitution p.Ile161Ser. This variant has been reported in many individuals with autosomal dominant epidermolysis bullosa, and has shown segregation in affected family members (Chan et al. 1993. PubMed ID: 7688477; Ehrlich et al. 1995. PubMed ID: 7537780; Pfendner et al. 2005. PubMed ID: 16098032). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at