rs1555978277

chrX-101359324-C-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_000061.3(BTK):c.863G>A(p.Arg288Gln) 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. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R288W) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 23)
• Consequence: BTK NM_000061.3 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 7.65

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]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a domain SH2 (size 96) in uniprot entity BTK_HUMAN there are 31 pathogenic changes around while only 0 benign (100%) in NM_000061.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-101359325-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 11366.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, BTK
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982
• PP5: Variant X-101359324-C-T is Pathogenic according to our data. Variant chrX-101359324-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 492813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101359324-C-T is described in Lovd as [Pathogenic]. Variant chrX-101359324-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTK	NM_000061.3	c.863G>A	p.Arg288Gln	missense_variant	10/19	ENST00000308731.8
BTK	NM_001287344.2	c.965G>A	p.Arg322Gln	missense_variant	10/19
BTK	NM_001287345.2	c.863G>A	p.Arg288Gln	missense_variant	11/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTK	ENST00000308731.8	c.863G>A	p.Arg288Gln	missense_variant	10/19	1	NM_000061.3	P3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Feb 05, 2019

The BTK c.863G>A; p.Arg288Gln variant (rs1555978277) is reported in the literature in numerous individuals with symptoms or a diagnosis of X-linked agammaglobulinemia (Abbott 2013, Conley 1998, Fiorini 2004, Futatani 2001, Lee 2010, Plebani 2002). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism, and it is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 492813). The arginine at codon 288 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Further, this variant occurs in the phosphotyrosine-binding pocket of a functional important SH2 domain and in vitro assays indicate that it disrupts binding to phosphorylated peptides (Tzeng 2000). Another variant at the same codon (p.Arg288Trp) has been reported in individuals with X-linked agammaglobulinemia and is considered pathogenic (Fiorini 2004, Plebani 2002, Tzeng 2000). Based on available information, the p.Arg288Gln variant is considered to be pathogenic. References: Abbott JK et al. Coding-region alterations in BTK do not universally cause X-linked agammaglobulinemia. J Allergy Clin Immunol. 2013 Nov;132(5):1246-8. Conley ME et al. Mutations in btk in patients with presumed X-linked agammaglobulinemia. Am J Hum Genet. 1998 May;62(5):1034-43. Fiorini M et al. BTK: 22 novel and 25 recurrent mutations in European patients with X-linked agammaglobulinemia. Hum Mutat. 2004 Mar;23(3):286. Futatani T et al. Bruton's tyrosine kinase is present in normal platelets and its absence identifies patients with X-linked agammaglobulinaemia and carrier females. Br J Haematol. 2001 Jul;114(1):141-9. Lee PP et al. Clinical characteristics and genotype-phenotype correlation in 62 patients with X-linked agammaglobulinemia. J Clin Immunol. 2010 Jan;30(1):121-31. Plebani A et al. Clinical, immunological, and molecular analysis in a large cohort of patients with X-linked agammaglobulinemia: an Italian multicenter study. Clin Immunol. 2002 Sep;104(3):221-30. Tzeng SR et al. Stability and peptide binding specificity of Btk SH2 domain: molecular basis for X-linked agammaglobulinemia. Protein Sci. 2000 Dec;9(12):2377-85. -

Autosomal recessive agammaglobulinemia 1 Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Mar 03, 2010

- -

X-linked agammaglobulinemia with growth hormone deficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 08, 2024

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 288 of the BTK protein (p.Arg288Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with X-linked agammaglobulinemia (PMID: 9545398, 11472359, 12217331, 15661032). ClinVar contains an entry for this variant (Variation ID: 492813). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BTK protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects BTK function (PMID: 11206059). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Nov 26, 2018

The R288Q variant has been published previously in association with X-linked agammaglobulinemia (Conley et al., 1998; Lavrador et al., 2014; García-García et al., 2016). The variant is not observed in large population cohorts (Lek et al., 2016). R288Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. Functional studies have shown that R288Q abolishes the SH2 domain's binding affinity to receptor tyrosine kinase (Tzeng et al., 2000). The SH2 domain is a known hotspot for BTK pathogenic variants, and a missense variant in the same residue (R288W) has been reported in the Human Gene Mutation Database in association with X-linked agammaglobulinemia (García-García et al., 2016; Stenson et al., 2014), supporting the functional importance of this region of the protein. In summary, we consider this variant to be pathogenic. -

X-linked agammaglobulinemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Nov 11, 2019

Variant summary: BTK c.863G>A (p.Arg288Gln) results in a conservative amino acid change located in the SH2 domain (IPR000980) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 183437 control chromosomes (gnomAD). c.863G>A has been reported in the literature in multiple individuals affected with X-linked Agammaglobulinemia (e.g. Chen_2016, Conley_1998, Esenboga_2018, Plebani_2002). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrate that the variant located in the phosphotyrosine binding site of the BTK SH2 domain results in total loss of the peptide binding affinity (Tzeng_2000). Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.65	D
BayesDel_noAF	Pathogenic	0.69
Cadd	Pathogenic	33
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.90	D;.;.;D
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.97	D;D;D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.64	T
Sift4G	Uncertain	0.0030	D;D;D;D
Polyphen		1.0	.;D;.;D
Vest4		0.87
MutPred		0.88		Loss of MoRF binding (P = 0.0423);Loss of MoRF binding (P = 0.0423);.;Loss of MoRF binding (P = 0.0423);
MVP		1.0
MPC		2.7
ClinPred		1.0	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.97
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1555978277; hg19: chrX-100614312; COSMIC: COSV58124345; COSMIC: COSV58124345;