X-154773143-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_Strong
The NM_001363.5(DKC1):c.1049T>C(p.Met350Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M350I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001363.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DKC1 | NM_001363.5 | c.1049T>C | p.Met350Thr | missense_variant | 11/15 | ENST00000369550.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKC1 | ENST00000369550.10 | c.1049T>C | p.Met350Thr | missense_variant | 11/15 | 1 | NM_001363.5 | P2 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 27
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Dyskeratosis congenita, X-linked Other:2
not provided, no classification provided | literature only | GeneReviews | - | - - |
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at