GPSM1

G protein signaling modulator 1, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 9:136327475-136359605

Links

ENSG00000160360 ∙ NCBI:26086 ∙ OMIM:609491 ∙ HGNC:17858 ∙ Uniprot:Q86YR5 ∙ 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 GPSM1 gene.

• Inborn genetic diseases (50 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPSM1 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						0
missense			50			50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	50	0	0

Variants in GPSM1

This is a list of pathogenic ClinVar variants found in the GPSM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136327712-C-T		not specified	Uncertain significance (Jun 29, 2023)
9-136327736-G-A		not specified	Uncertain significance (Jan 26, 2022)
9-136334541-G-A		not specified	Uncertain significance (May 03, 2023)
9-136334601-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-136334629-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-136334650-A-T		not specified	Uncertain significance (Jan 09, 2024)
9-136336067-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-136336924-G-A		not specified	Uncertain significance (Dec 06, 2021)
9-136336939-C-T		not specified	Uncertain significance (Jul 11, 2023)
9-136336950-C-G		not specified	Uncertain significance (Aug 03, 2022)
9-136336957-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-136336980-A-C		not specified	Uncertain significance (Mar 01, 2024)
9-136336996-G-A		not specified	Uncertain significance (Jul 30, 2023)
9-136337017-G-A		not specified	Uncertain significance (Oct 29, 2021)
9-136337039-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-136337475-C-T		not specified	Uncertain significance (Sep 12, 2023)
9-136337482-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-136337548-C-T		not specified	Uncertain significance (Jan 18, 2023)
9-136337847-G-A		not specified	Uncertain significance (Dec 02, 2022)
9-136337855-A-G		not specified	Uncertain significance (Nov 16, 2021)
9-136337885-G-A		not specified	Uncertain significance (Oct 30, 2023)
9-136337933-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-136337934-G-A		not specified	Uncertain significance (Feb 21, 2024)
9-136338574-C-T		not specified	Uncertain significance (Oct 22, 2021)
9-136338575-G-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPSM1	protein_coding	protein_coding	ENST00000440944	14	32126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000221	0.999	125426	0	13	125439	0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	420	443	0.947	0.0000316	4292
Missense in Polyphen		178	182.55	0.97506		1784
Synonymous	0.149	211	214	0.987	0.0000175	1354
Loss of Function	2.90	13	30.2	0.430	0.00000154	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000152
Ashkenazi Jewish	0.000203	0.000199
East Asian	0.0000559	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000454	0.0000441
Middle Eastern	0.0000559	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide dissociation inhibitor (GDI) which functions as a receptor-independent activator of heterotrimeric G- protein signaling. Keeps G(i/o) alpha subunit in its GDP-bound form thus uncoupling heterotrimeric G-proteins signaling from G protein-coupled receptors. Controls spindle orientation and asymmetric cell fate of cerebral cortical progenitors. May also be involved in macroautophagy in intestinal cells. May play a role in drug addiction. {ECO:0000269|PubMed:11024022, ECO:0000269|PubMed:12642577}.
• Pathway: Cocaine addiction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.0682
• rvis_EVS: -1.32
• rvis_percentile_EVS: 4.73

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.319
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpsm1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); renal/urinary system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: nervous system development;positive regulation of macroautophagy;cell differentiation;negative regulation of GTPase activity;negative regulation of guanyl-nucleotide exchange factor activity
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cytosol;plasma membrane;cell cortex;protein-containing complex
• Molecular function: GDP-dissociation inhibitor activity;protein binding