rs128620186
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate
The NM_000061.3(BTK):c.2T>C(p.Met1?) variant causes a start lost 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. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 22)
Consequence
BTK
NM_000061.3 start_lost
NM_000061.3 start_lost
Scores
6
3
2
Clinical Significance
Conservation
PhyloP100: 7.72
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 14 ACMG points.
PVS1
?
Start lost variant, no new inframe start found.
PS1
?
Another start lost variant in NM_000061.3 (BTK) was described as [Pathogenic] in ClinVar as 863382
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-101375283-A-G is Pathogenic according to our data. Variant chrX-101375283-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 11349.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-101375283-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BTK | NM_000061.3 | c.2T>C | p.Met1? | start_lost | 2/19 | ENST00000308731.8 | |
BTK | NM_001287345.2 | c.2T>C | p.Met1? | start_lost | 3/17 | ||
BTK | NM_001287344.2 | c.104T>C | p.Met35Thr | missense_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTK | ENST00000308731.8 | c.2T>C | p.Met1? | start_lost | 2/19 | 1 | NM_000061.3 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
X-linked agammaglobulinemia with growth hormone deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2022 | This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 11349). Disruption of the initiator codon has been observed in individuals with clinical features of BTK-related conditions (PMID: 7849697, 8644706, 10737994, 23335184). It has also been observed to segregate with disease in related individuals. This sequence change affects the initiator methionine of the BTK mRNA. The next in-frame methionine is located at codon 89. - |
X-linked agammaglobulinemia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 1996 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.;T
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;T;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
A;A
Sift4G
Pathogenic
D;D;D;D
Polyphen
0.46, 0.97
.;P;.;D
Vest4
MutPred
Gain of catalytic residue at M1 (P = 0.007);Gain of catalytic residue at M1 (P = 0.007);.;Gain of catalytic residue at M1 (P = 0.007);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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