rs36022183
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000379989.6(CDKL5):c.3003C>G(p.His1001Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign 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. H1001D) has been classified as Likely benign.
Frequency
Consequence
ENST00000379989.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.184+3199G>C | intron_variant | ENST00000379984.4 | |||
CDKL5 | NM_001037343.2 | c.3003C>G | p.His1001Gln | missense_variant | 22/22 | ||
CDKL5 | NM_003159.3 | c.3003C>G | p.His1001Gln | missense_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000379989.6 | c.3003C>G | p.His1001Gln | missense_variant | 22/22 | 1 | |||
CDKL5 | ENST00000379996.7 | c.3003C>G | p.His1001Gln | missense_variant | 21/21 | 1 | |||
RS1 | ENST00000379984.4 | c.184+3199G>C | intron_variant | 1 | NM_000330.4 | P1 | |||
CDKL5 | ENST00000673617.1 | n.275C>G | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | RettBASE | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at