17-40819085-C-CG
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_000421.5(KRT10):c.1449_1450insC(p.Gly484ArgfsTer97) 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 Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
KRT10
NM_000421.5 frameshift
NM_000421.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.47
Genes affected
KRT10 (HGNC:6413): (keratin 10) This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-40819085-C-CG is Pathogenic according to our data. Variant chr17-40819085-C-CG is described in ClinVar as [Pathogenic]. Clinvar id is 14583.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| KRT10 | NM_000421.5 | c.1449_1450insC | p.Gly484ArgfsTer97 | frameshift_variant | 7/8 | ENST00000269576.6 | NP_000412.4 | |
| KRT10 | NM_001379366.1 | c.1449_1450insC | p.Gly484ArgfsTer97 | frameshift_variant | 7/8 | NP_001366295.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| KRT10 | ENST00000269576.6 | c.1449_1450insC | p.Gly484ArgfsTer97 | frameshift_variant | 7/8 | 1 | NM_000421.5 | ENSP00000269576 | P2 | |
| KRT10-AS1 | ENST00000301665.9 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Congenital reticular ichthyosiform erythroderma Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2010 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at