NM_000397.4(CYBB):c.603C>G (p.Tyr201Ter) AND Granulomatous disease, chronic, X-linked

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 28, 2020
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:: RCV001389980.7

Allele description [Variation Report for NM_000397.4(CYBB):c.603C>G (p.Tyr201Ter)]

NM_000397.4(CYBB):c.603C>G (p.Tyr201Ter)

Gene:

CYBB:cytochrome b-245 beta chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_000397.4(CYBB):c.603C>G (p.Tyr201Ter)

HGVS:

NC_000023.11:g.37796070C>G
NG_009065.1:g.21050C>G
NM_000397.4:c.603C>GMANE SELECT
NP_000388.2:p.Tyr201Ter
LRG_53:g.21050C>G
NC_000023.10:g.37655323C>G

Protein change:

Y201*

Links:

dbSNP: rs2146811786

NCBI 1000 Genomes Browser:

rs2146811786

Molecular consequence:

NM_000397.4:c.603C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Granulomatous disease, chronic, X-linked
Synonyms:: CYTOCHROME b-NEGATIVE GRANULOMATOUS DISEASE, CHRONIC, X-LINKED; GRANULOMATOUS DISEASE, CHRONIC, X-LINKED, SOMATIC MOSAIC
Identifiers:: MONDO: MONDO:0010600; MedGen: C1844376; Orphanet: 379; OMIM: 306400

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long-chain fatty acid--CoA ligase [Mucilaginibacter xinganensis]
long-chain fatty acid--CoA ligase [Mucilaginibacter xinganensis]
gi|1233021305|gnl|Haust|MuYL_4852|g 36735.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001591544	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 28, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9585602, 20729109, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591544

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 28, 2020)

germline

clinical testing

PubMed (3)
[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

X-Linked chronic granulomatous disease: mutations in the CYBB gene encoding the gp91-phox component of respiratory-burst oxidase.

Rae J, Newburger PE, Dinauer MC, Noack D, Hopkins PJ, Kuruto R, Curnutte JT.

Am J Hum Genet. 1998 Jun;62(6):1320-31.

PubMed [citation]

PMID:: 9585602
PMCID:: PMC1377153

Hematologically important mutations: X-linked chronic granulomatous disease (third update).

Roos D, Kuhns DB, Maddalena A, Roesler J, Lopez JA, Ariga T, Avcin T, de Boer M, Bustamante J, Condino-Neto A, Di Matteo G, He J, Hill HR, Holland SM, Kannengiesser C, Köker MY, Kondratenko I, van Leeuwen K, Malech HL, Marodi L, Nunoi H, Stasia MJ, et al.

Blood Cells Mol Dis. 2010 Oct 15;45(3):246-65. doi: 10.1016/j.bcmd.2010.07.012. Epub 2010 Aug 21. Review.

PubMed [citation]

PMID:: 20729109
PMCID:: PMC4360070

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001591544.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in CYBB are known to be pathogenic (PMID: 9585602, 20729109). This variant has been observed in individual(s) with chronic granulomatous disease (PMID: 20729109). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr201*) in the CYBB gene. It is expected to result in an absent or disrupted protein product.

#	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: Sep 29, 2024

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