13-26254729-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_001260.3(CDK8):c.88G>A(p.Gly30Ser) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G30C) has been classified as Pathogenic.
Frequency
Consequence
NM_001260.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK8 | NM_001260.3 | c.88G>A | p.Gly30Ser | missense_variant | 1/13 | ENST00000381527.8 | |
CDK8 | NM_001318368.2 | c.88G>A | p.Gly30Ser | missense_variant | 1/13 | ||
CDK8 | NM_001346501.2 | c.-374G>A | 5_prime_UTR_variant | 1/12 | |||
CDK8 | XM_047430033.1 | c.-143G>A | 5_prime_UTR_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK8 | ENST00000381527.8 | c.88G>A | p.Gly30Ser | missense_variant | 1/13 | 1 | NM_001260.3 | P1 | |
CDK8 | ENST00000536792.5 | c.88G>A | p.Gly30Ser | missense_variant, NMD_transcript_variant | 1/12 | 1 | |||
CDK8 | ENST00000700501.1 | c.88G>A | p.Gly30Ser | missense_variant, NMD_transcript_variant | 1/12 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Intellectual developmental disorder with hypotonia and behavioral abnormalities Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at