GNGT1

protein-coding

G protein subunit gamma transducin 1, the group of G protein subunits gamma

Gene summary

This gene encodes the gamma subunit of transducin, a guanine nucleotide-binding protein (G protein) that is found in rod outer segments. Transducin, also known as GMPase, mediates the activation of a cyclic GTP-specific (guanosine monophosphate) phosphodiesterase by rhodopsin. [provided by RefSeq, Jul 2016]

MANE transcript

NM_021955.5

Inheritance

—

ClinVar variants

U:9

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr7:93,591,573-93,911,265

External References & Databases

Ensembl (ENSG00000127928)

Transcript & Mutation Effects

hg38 • Region Span ~319.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GNGT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021955.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			8 clinvar			8
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	9	0	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021955.5	RefSeq	NP_068774.1	2	MANE Select
ENST00000248572.10	Ensembl	ENSP00000248572.5	2	MANE Select
NM_001329426.2	RefSeq	NP_001316355.1	2	Standard
ENST00000428834.1	Ensembl	ENSP00000401781.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
Relaxin signaling pathway - Homo sapiens (human)
Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
Retrograde endocannabinoid signaling - Homo sapiens (human)
GABAergic synapse - Homo sapiens (human)

Biological Process

signal transduction
phototransduction
protein localization
cardiac muscle cell apoptotic process
rhodopsin mediated signaling pathway

Molecular Function

GTPase activity
protein binding

Cellular Component

photoreceptor outer segment
photoreceptor inner segment
heterotrimeric G-protein complex
plasma membrane
photoreceptor disc membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000248572
Coding exons: 2
Length: 319693
Individuals with no LoFs: 125625
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125632
p: 0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.619	47	36.5	1.29	0.00000167	478
Missense (PolyPhen)		12	10.558	1.1366		152
Synonymous	-0.617	17	14.1	1.21	7.60e-7	129
Loss of Function	1.22	1	3.44	0.291	2.42e-7	39

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000058	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein- effector interaction.;

Recessive Scores

pRec: 0.178

Intolerance Scores

LoFtool: 0.283
RVIS EVS: 0.19
RVIS percentile EVS: 66.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Low	Medium