NM_000061.3(BTK):c.1688G>A (p.Trp563Ter) AND X-linked agammaglobulinemia with growth hormone deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 22, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000702940.6

Allele description [Variation Report for NM_000061.3(BTK):c.1688G>A (p.Trp563Ter)]

NM_000061.3(BTK):c.1688G>A (p.Trp563Ter)

Gene:

BTK:Bruton tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq22.1

Genomic location:

Preferred name:

NM_000061.3(BTK):c.1688G>A (p.Trp563Ter)

HGVS:

NC_000023.11:g.101353932C>T
NG_009616.1:g.37293G>A
NG_011734.1:g.38G>A
NM_000061.3:c.1688G>AMANE SELECT
NM_001287344.2:c.1790G>A
NM_001287345.2:c.1160G>A
NP_000052.1:p.Trp563Ter
NP_000052.1:p.Trp563Ter
NP_001274273.1:p.Trp597Ter
NP_001274274.1:p.Trp387Ter
LRG_128t1:c.1688G>A
LRG_128:g.37293G>A
LRG_128p1:p.Trp563Ter
NC_000023.10:g.100608920C>T
NM_000061.2:c.1688G>A

Protein change:

W387*

Links:

dbSNP: rs1555977474

NCBI 1000 Genomes Browser:

rs1555977474

Molecular consequence:

NM_000061.3:c.1688G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001287344.2:c.1790G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001287345.2:c.1160G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: X-linked agammaglobulinemia with growth hormone deficiency (IGHD3)
Synonyms:: IGHD III; Isolated growth hormone deficiency type 3; Growth hormone deficiency with hypogammaglobulinemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010615; MedGen: C0472813; Orphanet: 631; OMIM: 307200

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SAOUHSC_00083 [Staphylococcus aureus subsp. aureus NCTC 8325]
SAOUHSC_00083 [Staphylococcus aureus subsp. aureus NCTC 8325]
Gene ID:3919461

Gene
YP_498683 AND (alive[prop]) (1)
Gene
Glycine max microRNA MIR10413b (MIR10413B), microRNA
Glycine max microRNA MIR10413b (MIR10413B), microRNA
gi|1620864251|ref|NR_161682.1|

Nucleotide
Mus musculus olfactomedin 1 (Olfm1), transcript variant 1, mRNA
Mus musculus olfactomedin 1 (Olfm1), transcript variant 1, mRNA
gi|84370356|ref|NM_019498.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000831817	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 22, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 9445504, 15661032, 16862044, 19419768, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000831817

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 22, 2022)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation screening of the BTK gene in 56 families with X-linked agammaglobulinemia (XLA): 47 unique mutations without correlation to clinical course.

Holinski-Feder E, Weiss M, Brandau O, Jedele KB, Nore B, Bäckesjö CM, Vihinen M, Hubbard SR, Belohradsky BH, Smith CI, Meindl A.

Pediatrics. 1998 Feb;101(2):276-84.

PubMed [citation]

PMID:: 9445504

Genetic analysis of patients with defects in early B-cell development.

Conley ME, Broides A, Hernandez-Trujillo V, Howard V, Kanegane H, Miyawaki T, Shurtleff SA.

Immunol Rev. 2005 Feb;203:216-34. Review.

PubMed [citation]

PMID:: 15661032

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000831817.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 579604). This premature translational stop signal has been observed in individual(s) with X-linked agammaglobulinemia (XLA) (PMID: 9445504). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp563*) 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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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