X-101356176-C-G

Variant names:

• chrX-101356176-C-G
• rs1057519825
• NM_000061.3:c.1442G>C

Variant summary

Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PS1_Moderate PM2 PP2 PP3_Moderate PP5

The NM_000061.3(BTK):​c.1442G>C​(p.Cys481Ser) 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 Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in ClinVar.

• Frequency: Genomes: not found (cov: 22)
• Consequence: BTK NM_000061.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:2
• Conservation: PhyloP100: 6.17
• Publications: 463 publications found

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]

BTK Gene-Disease associations (from GenCC):

• Bruton-type agammaglobulinemia

  Inheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: Myriad Women’s Health, Orphanet, ClinGen
• isolated growth hormone deficiency type III

  Inheritance: XL Classification: STRONG, NO_KNOWN Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
• short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemia

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_pathogenic. The variant received 8 ACMG points.

• PS1: Transcript NM_000061.3 (BTK) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar.
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 90 curated pathogenic missense variants (we use a threshold of 10). The gene has 26 curated benign missense variants. Gene score misZ: 4.0394 (above the threshold of 3.09). Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to Bruton-type agammaglobulinemia, short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemia, isolated growth hormone deficiency type III.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.893
• PP5: Variant X-101356176-C-G is Pathogenic according to our data. Variant chrX-101356176-C-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 376203.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTK	NM_000061.3	c.1442G>C	p.Cys481Ser	missense_variant	Exon 15 of 19	ENST00000308731.8	NP_000052.1
BTK	NM_001287344.2	c.1544G>C	p.Cys515Ser	missense_variant	Exon 15 of 19		NP_001274273.1
BTK	NM_001287345.2	c.1039-1482G>C		intron_variant	Intron 13 of 16		NP_001274274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTK	ENST00000308731.8	c.1442G>C	p.Cys481Ser	missense_variant	Exon 15 of 19	1	NM_000061.3	ENSP00000308176.8

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Malignant lymphoma, large B-cell, diffuse Pathogenic:1

Jul 25, 2023

Wasik Lab, Fox Chase Cancer Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant was observed in a patient with DLBCL that presented in leukemic form, best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial good clinical response to BTK inhibitor ibrutinib, anti-CD20 antibody rituxan, alkylating agent bendamustine, and hematopoietic stem-cell transplant, the lymphoma relapsed, accompanied by morphologic and molecular evidence of disease progression. BTK is an essential component of the BCR-activated signaling pathway. At presentation, this tumor had increased DNA copy number for BTK, likely indicating dependency on BCR signaling. The recurrent tumor developed the BTK C481S mutation associated with BTK inhibitor resistance, which alters the binding site for ibrutinib, rendering the drug ineffective (George et al. 2020; Ondrisova and Mraz 2020). This has been well-described in chronic lymphocytic leukemia and other lymphoid malignancies (Nakhoda et al. 2023). The effect of BTK C481S mutation-based resistance to ibrutinib seemed in this case to be further amplified by copy number gain of the BTK gene through tetraploidy of chromosome X. The BTK-encoding region of chromosome X partially lost this amplification at relapse. This may represent a mechanism to decrease BTK signaling dependence as an additional route to ibrutinib resistance. However, the strong expression of BTK at relapse indicated that the BTK mutation, not BTK-independence, was overall responsible for ibrutinib becoming ineffective. -

not provided Pathogenic:1

Sep 13, 2017

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1

Jan 28, 2025

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: BTK c.1442G>C (p.Cys481Ser) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) 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 183410 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, c.1442G>C has not been reported in the literature as a germline change in individuals affected with X-linked Agammaglobulinemia. However, this variant and others resulting in a C481S BTK protein have been detected in patients with chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) who developed resistance to ibrutinib therapy (Ahn_2017, Albitar_2017, Burger_2016, Chiron_2014, Woyach_2014,2017). These reports do not provide unequivocal conclusions about association of the variant with X-linked Agammaglobulinemia. Several publications report experimental evidence that the variant impairs binding of ibrutinib, rescuing BTK signaling in cells treated with the drug (Chiron_2014, Chen_2018, Cheng_2014, Woyach_2014). However, no significant differences in downstream signaling were observed in DT40 (BTK-/-) chicken B cells transfected with wild type or C481S BTK in the absence of ibutinib (Woyach_2014). Thus, the variant's effects on the protein appear to be limited to ibrutinib binding, and these assays cannot be used to predict the consequences of the variant as a germline mutation. The following publications have been ascertained in the context of this evaluation (PMID: 28418267, 25189416, 25082755, 28049639, 28212557, 27199251, 29496671, 24869598). ClinVar contains an entry for this variant (Variation ID: 376203 ). Based on the evidence outlined above, the variant was classified as uncertain significance. -

X-linked agammaglobulinemia with growth hormone deficiency Uncertain:1

Oct 25, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces cysteine with serine at codon 481 of the BTK protein (p.Cys481Ser). The cysteine residue is highly conserved and there is a moderate physicochemical difference between cysteine and serine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature as a germline variant in individuals with BTK-related conditions. ClinVar contains an entry for this variant (Variation ID: 376203). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.60
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.060
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.71	D;.;D
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.92	D;D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Pathogenic	0.89	D;D;D
MetaSVM	Uncertain	0.20	D
MutationAssessor	Benign	-1.3	.;.;N
PhyloP100		6.2
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-7.0	.;.;D
REVEL	Uncertain	0.52
Sift	Benign	0.31	.;.;T
Sift4G	Benign	0.23	T;T;T
Polyphen		0.98	.;.;D
Vest4		0.77
MutPred		0.64		Loss of catalytic residue at L482 (P = 0.0168);.;Loss of catalytic residue at L482 (P = 0.0168);
MVP		0.91
MPC		2.6
ClinPred		0.95	D
GERP RS		5.6
Varity_R		0.94
gMVP		0.97
Mutation Taster		=26/74	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1057519825; hg19: chrX-100611164; COSMIC: COSV58117136;