rs797045142
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_000494.4(COL17A1):c.2816C>T(p.Thr939Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_000494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL17A1 | NM_000494.4 | c.2816C>T | p.Thr939Ile | missense_variant | 42/56 | ENST00000648076.2 | NP_000485.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL17A1 | ENST00000648076.2 | c.2816C>T | p.Thr939Ile | missense_variant | 42/56 | NM_000494.4 | ENSP00000497653 | A2 | ||
COL17A1 | ENST00000369733.8 | c.2762-492C>T | intron_variant | 5 | ENSP00000358748 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 38 AF XY: 0.00 AC XY: 0AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 04, 2023 | This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 939 of the COL17A1 protein (p.Thr939Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant epithelial recurrent erosion dystrophy (PMID: 25676728). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 208977). 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 not expected to disrupt COL17A1 protein function. For these reasons, this variant has been classified as Pathogenic. - |
Epithelial recurrent erosion dystrophy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at