GPSM3

G protein signaling modulator 3

Basic information

Region (hg38): 6:32190765-32195523

Previous symbols: [ "C6orf9" ]

Links

ENSG00000213654 ∙ NCBI:63940 ∙ OMIM:618558 ∙ HGNC:13945 ∙ Uniprot:Q9Y4H4 ∙ 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 GPSM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPSM3 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			8	2	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	8	2	4

Variants in GPSM3

This is a list of pathogenic ClinVar variants found in the GPSM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32191414-C-T			Benign (May 25, 2018)
6-32191437-A-C		not specified	Uncertain significance (Oct 10, 2023)
6-32191828-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-32191833-G-A		not specified	Uncertain significance (May 30, 2023)
6-32191842-T-C		not specified	Uncertain significance (Jul 06, 2021)
6-32192154-G-C			Benign (May 25, 2018)
6-32192156-C-T		not specified	Likely benign (Sep 12, 2023)
6-32192157-G-A		not specified	Uncertain significance (Nov 06, 2023)
6-32192168-G-A		not specified	Uncertain significance (Apr 24, 2024)
6-32192222-G-A		not specified	Uncertain significance (Dec 12, 2023)
6-32192244-G-A		not specified	Likely benign (May 17, 2023)
6-32192473-T-G		not specified	Uncertain significance (Dec 21, 2022)
6-32194075-G-A			Benign (Oct 29, 2020)
6-32195497-G-A			Benign (May 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPSM3	protein_coding	protein_coding	ENST00000375040	4	4758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.286	0.694	125548	0	14	125562	0.0000558

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.865	67	90.1	0.744	0.00000539	986
Missense in Polyphen		23	38.276	0.60089		399
Synonymous	1.98	19	33.6	0.565	0.00000160	346
Loss of Function	1.97	2	8.00	0.250	4.17e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000718	0.0000718
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000951	0.0000881
Middle Eastern	0.00	0.00
South Asian	0.0000689	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with subunit of G(i) alpha proteins and regulates the activation of G(i) alpha proteins. {ECO:0000269|PubMed:14656218, ECO:0000269|PubMed:15096500}.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.492
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.318
• hipred: N
• hipred_score: 0.337
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.803

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpsm3
• Phenotype: immune system phenotype; cellular phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; skeleton phenotype

Gene ontology

• Biological process: positive regulation of leukocyte chemotaxis;biological_process;positive regulation of inflammatory response;regulation of catalytic activity;positive regulation of cytokine production involved in inflammatory response
• Cellular component: cellular_component;cytoplasm;plasma membrane
• Molecular function: molecular_function;protein binding;GTPase regulator activity