NM_006019.4(TCIRG1):c.1480C>T (p.Gln494Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 19, 2023
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:: RCV003699112.2

Allele description [Variation Report for NM_006019.4(TCIRG1):c.1480C>T (p.Gln494Ter)]

NM_006019.4(TCIRG1):c.1480C>T (p.Gln494Ter)

Gene:

TCIRG1:T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_006019.4(TCIRG1):c.1480C>T (p.Gln494Ter)

HGVS:

NC_000011.10:g.68047898C>T
NG_007878.1:g.13883C>T
NM_001351059.2:c.586C>T
NM_006019.4:c.1480C>TMANE SELECT
NM_006053.4:c.832C>T
NP_001337988.1:p.Gln196Ter
NP_006010.2:p.Gln494Ter
NP_006010.2:p.Gln494Ter
NP_006044.1:p.Gln278Ter
LRG_115t1:c.1480C>T
LRG_115:g.13883C>T
LRG_115p1:p.Gln494Ter
NC_000011.9:g.67815365C>T
NM_006019.2:c.1480C>T

Protein change:

Q196*

Molecular consequence:

NM_001351059.2:c.586C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006019.4:c.1480C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006053.4:c.832C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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ribosomal protein L32 (chloroplast) [Astragalus hezarensis]
ribosomal protein L32 (chloroplast) [Astragalus hezarensis]
gi|1941598715|dbj|BCA90184.1|

Protein
Nucleotide Links for GEO Profiles (Select 93672121) (7)
Nucleotide
Taxonomy Links for Protein (Select 528894510) (1)
Taxonomy
Taxonomy Links for Protein (Select 30411083) (1)
Taxonomy
Coelidiinae wingless (Wg) gene, partial cds.
Coelidiinae wingless (Wg) gene, partial cds.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004470925	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 19, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 10888887, 10942435, 11532986, 19448635, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004470925

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 19, 2023)

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

Defects in TCIRG1 subunit of the vacuolar proton pump are responsible for a subset of human autosomal recessive osteopetrosis.

Frattini A, Orchard PJ, Sobacchi C, Giliani S, Abinun M, Mattsson JP, Keeling DJ, Andersson AK, Wallbrandt P, Zecca L, Notarangelo LD, Vezzoni P, Villa A.

Nat Genet. 2000 Jul;25(3):343-6.

PubMed [citation]

PMID:: 10888887

Mutations in the a3 subunit of the vacuolar H(+)-ATPase cause infantile malignant osteopetrosis.

Kornak U, Schulz A, Friedrich W, Uhlhaas S, Kremens B, Voit T, Hasan C, Bode U, Jentsch TJ, Kubisch C.

Hum Mol Genet. 2000 Aug 12;9(13):2059-63.

PubMed [citation]

PMID:: 10942435

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004470925.1

#	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. This variant has not been reported in the literature in individuals affected with TCIRG1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln494*) in the TCIRG1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TCIRG1 are known to be pathogenic (PMID: 10888887, 10942435, 11532986, 19448635).

#	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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