GNA15

G protein subunit alpha 15, the group of G protein subunits alpha, group q

Basic information

Region (hg38): 19:3136032-3163749

Links

ENSG00000060558 ∙ NCBI:2769 ∙ OMIM:139314 ∙ HGNC:4383 ∙ Uniprot:P30679 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GNA15 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GNA15 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			15		2	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	3

Variants in GNA15

This is a list of pathogenic ClinVar variants found in the GNA15 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-3136461-C-T		not specified	Uncertain significance (Jul 14, 2022)
19-3136473-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-3136498-G-C		not specified	Uncertain significance (May 11, 2022)
19-3148647-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-3148650-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-3148657-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-3148660-A-T		not specified	Uncertain significance (Feb 27, 2024)
19-3148723-T-C		not specified	Uncertain significance (Mar 01, 2023)
19-3150141-G-A			Benign (Dec 04, 2018)
19-3150267-T-A		not specified	Uncertain significance (Mar 07, 2023)
19-3151717-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-3151725-G-T		not specified	Uncertain significance (Nov 17, 2023)
19-3151726-C-T		not specified	Uncertain significance (Nov 17, 2022)
19-3151765-G-A		not specified	Uncertain significance (Sep 22, 2022)
19-3151771-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-3151782-G-A			Benign (Dec 04, 2018)
19-3151816-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-3151825-A-G		not specified	Uncertain significance (Mar 27, 2023)
19-3157732-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-3157796-C-T			Benign (Dec 04, 2018)
19-3157831-A-G		not specified	Uncertain significance (Sep 12, 2023)
19-3162870-G-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GNA15	protein_coding	protein_coding	ENST00000262958	7	27577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00597	0.990	125729	1	17	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	200	253	0.792	0.0000176	2428
Missense in Polyphen		66	92.759	0.71152		887
Synonymous	-0.601	117	109	1.07	0.00000810	714
Loss of Function	2.51	7	18.8	0.373	9.84e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000907	0.0000791
Middle Eastern	0.0000554	0.0000544
South Asian	0.0000704	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems.
• Pathway: Relaxin signaling pathway - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Endothelin Pathways;Human Complement System;G Protein Signaling Pathways;Signaling by GPCR;Signal Transduction;Thromboxane signalling through TP receptor;Metabolism;Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion;Acetylcholine regulates insulin secretion;Free fatty acids regulate insulin secretion;Regulation of insulin secretion;Signal amplification;Thrombin signalling through proteinase activated receptors (PARs);Platelet activation, signaling and aggregation;ADP signalling through P2Y purinoceptor 1;fmlp induced chemokine gene expression in hmc-1 cells;Hemostasis;Thromboxane A2 receptor signaling;Integration of energy metabolism;G alpha (q) signalling events;GPCR downstream signalling;PAR4-mediated thrombin signaling events;PAR1-mediated thrombin signaling events;LPA receptor mediated events;IL8- and CXCR1-mediated signaling events;S1P3 pathway;Arf6 signaling events;Plasma membrane estrogen receptor signaling;Sphingosine 1-phosphate (S1P) pathway;Endothelins;IL8- and CXCR2-mediated signaling events;S1P2 pathway (Consensus)

Intolerance Scores

• loftool: 0.105
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.0681
• hipred: Y
• hipred_score: 0.775
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gna15
• Phenotype: normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;activation of phospholipase C activity;phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway;platelet activation;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;phospholipase C-activating dopamine receptor signaling pathway
• Cellular component: heterotrimeric G-protein complex;plasma membrane
• Molecular function: G protein-coupled receptor binding;GTPase activity;GTP binding;G-protein beta/gamma-subunit complex binding;metal ion binding