NM_144499.3(GNAT1):c.273C>A (p.Tyr91Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 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:: RCV001388651.4

Allele description [Variation Report for NM_144499.3(GNAT1):c.273C>A (p.Tyr91Ter)]

NM_144499.3(GNAT1):c.273C>A (p.Tyr91Ter)

Gene:

GNAT1:G protein subunit alpha transducin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_144499.3(GNAT1):c.273C>A (p.Tyr91Ter)

HGVS:

NC_000003.12:g.50193388C>A
NG_009831.1:g.6779C>A
NM_000172.4:c.273C>A
NM_144499.3:c.273C>AMANE SELECT
NP_000163.2:p.Tyr91Ter
NP_653082.1:p.Tyr91Ter
NC_000003.11:g.50230821C>A

Protein change:

Y91*

Links:

dbSNP: rs143481438

NCBI 1000 Genomes Browser:

rs143481438

Molecular consequence:

NM_000172.4:c.273C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_144499.3:c.273C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001589724	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 22, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11095744, 31736247, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001589724

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 22, 2022)

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

Phototransduction in transgenic mice after targeted deletion of the rod transducin alpha -subunit.

Calvert PD, Krasnoperova NV, Lyubarsky AL, Isayama T, Nicoló M, Kosaras B, Wong G, Gannon KS, Margolskee RF, Sidman RL, Pugh EN Jr, Makino CL, Lem J.

Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13913-8. Erratum in: Proc Natl Acad Sci U S A 2001 Aug 28;98(18):10515.

PubMed [citation]

PMID:: 11095744
PMCID:: PMC17675

Extensive genic and allelic heterogeneity underlying inherited retinal dystrophies in Mexican patients molecularly analyzed by next-generation sequencing.

Zenteno JC, García-Montaño LA, Cruz-Aguilar M, Ronquillo J, Rodas-Serrano A, Aguilar-Castul L, Matsui R, Vencedor-Meraz CI, Arce-González R, Graue-Wiechers F, Gutiérrez-Paz M, Urrea-Victoria T, de Dios Cuadras U, Chacón-Camacho OF.

Mol Genet Genomic Med. 2020 Jan;8(1). doi: 10.1002/mgg3.1044. Epub 2019 Nov 17.

PubMed [citation]

PMID:: 31736247
PMCID:: PMC6978239

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001589724.3

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 1075132). This variant has not been reported in the literature in individuals affected with GNAT1-related conditions. This variant is present in population databases (rs143481438, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Tyr91*) in the GNAT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNAT1 are known to be pathogenic (PMID: 11095744, 31736247).

#	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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