rs199422249
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP2PP3_Moderate
The NM_001363.5(DKC1):c.1075G>A(p.Asp359Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,206,579 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
NM_001363.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DKC1 | NM_001363.5 | c.1075G>A | p.Asp359Asn | missense_variant | 11/15 | ENST00000369550.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DKC1 | ENST00000369550.10 | c.1075G>A | p.Asp359Asn | missense_variant | 11/15 | 1 | NM_001363.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000905 AC: 1AN: 110446Hom.: 0 Cov.: 22 AF XY: 0.0000306 AC XY: 1AN XY: 32710
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183378Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67808
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096133Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 361553
GnomAD4 genome ? AF: 0.00000905 AC: 1AN: 110446Hom.: 0 Cov.: 22 AF XY: 0.0000306 AC XY: 1AN XY: 32710
ClinVar
Submissions by phenotype
Dyskeratosis congenita, X-linked Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at