rs1555980049
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000061.3(BTK):c.371G>A(p.Trp124*) variant causes a stop gained 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 (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 23)
Consequence
BTK
NM_000061.3 stop_gained
NM_000061.3 stop_gained
Scores
3
1
1
Clinical Significance
Conservation
PhyloP100: 7.01
Genes affected
BTK (HGNC:1133): (Bruton tyrosine kinase) The protein encoded by this gene plays a crucial role in B-cell development. Mutations in this gene cause X-linked agammaglobulinemia type 1, which is an immunodeficiency characterized by the failure to produce mature B lymphocytes, and associated with a failure of Ig heavy chain rearrangement. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-101370018-C-T is Pathogenic according to our data. Variant chrX-101370018-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 492811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101370018-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTK | NM_000061.3 | c.371G>A | p.Trp124* | stop_gained | 5/19 | ENST00000308731.8 | NP_000052.1 | |
BTK | NM_001287344.2 | c.473G>A | p.Trp158* | stop_gained | 5/19 | NP_001274273.1 | ||
BTK | NM_001287345.2 | c.371G>A | p.Trp124* | stop_gained | 6/17 | NP_001274274.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTK | ENST00000308731.8 | c.371G>A | p.Trp124* | stop_gained | 5/19 | 1 | NM_000061.3 | ENSP00000308176.8 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome Cov.: 23
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive agammaglobulinemia 1 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital | Jul 21, 2009 | - - |
X-linked agammaglobulinemia with growth hormone deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 10, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 492811). This variant is also known as 503G>A. This premature translational stop signal has been observed in individual(s) with X-linked agammaglobulinemia (PMID: 8695804). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp124*) in the BTK gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BTK are known to be pathogenic (PMID: 15661032, 16862044, 19419768). - |
X-linked agammaglobulinemia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 24, 2017 | Variant summary: The BTK c.371G>A (p.Trp124X) variant results in a premature termination codon, predicted to cause a truncated or absent BTK protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.982C>T, p.Gln328X; c.1455C>A, p.Tyr485X; c.1558C>T, p.Arg520X). One in silico tool predicts a damaging outcome for this variant. This variant is absent in 86517 control chromosomes but has been reported in at least 2 affected individuals in the literature (Wang_2009, Hashimoto_1996). Taken together, this variant is classified as likely pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
FATHMM_MKL
Pathogenic
D
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at