X-101353935-C-T
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Moderate
The NM_000061.3(BTK):c.1685G>A(p.Arg562Gln) variant causes a missense change. 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R562P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000061.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTK | NM_000061.3 | c.1685G>A | p.Arg562Gln | missense_variant | Exon 17 of 19 | ENST00000308731.8 | NP_000052.1 | |
BTK | NM_001287344.2 | c.1787G>A | p.Arg596Gln | missense_variant | Exon 17 of 19 | NP_001274273.1 | ||
BTK | NM_001287345.2 | c.1157G>A | p.Arg386Gln | missense_variant | Exon 15 of 17 | NP_001274274.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
X-linked agammaglobulinemia Pathogenic:1
ACMG classification criteria: PM2 moderated, PM5 moderated, PP2 supporting, PP3 supporting -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.