RIMBP2

RIMS binding protein 2, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 12:130396132-130768228

Links

ENSG00000060709 ∙ NCBI:23504 ∙ OMIM:611602 ∙ HGNC:30339 ∙ Uniprot:O15034 ∙ 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 RIMBP2 gene.

• Inborn genetic diseases (45 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIMBP2 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				7		7
missense			40	5	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	12	1

Variants in RIMBP2

This is a list of pathogenic ClinVar variants found in the RIMBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-130399152-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-130399745-T-G		not specified	Uncertain significance (Sep 01, 2021)
12-130399786-C-G		not specified	Uncertain significance (Dec 18, 2023)
12-130406192-C-T		not specified	Uncertain significance (Jul 22, 2022)
12-130406216-T-C		not specified	Uncertain significance (Nov 10, 2022)
12-130406221-C-G		not specified	Uncertain significance (Jun 27, 2022)
12-130406233-G-A		not specified	Uncertain significance (May 24, 2023)
12-130407728-C-T		not specified	Uncertain significance (Sep 15, 2021)
12-130407805-C-T		not specified	Likely benign (Oct 10, 2023)
12-130407806-G-A		not specified	Uncertain significance (Dec 01, 2022)
12-130414231-G-A		not specified	Uncertain significance (May 23, 2023)
12-130414289-G-A		not specified	Uncertain significance (Nov 02, 2023)
12-130414294-C-T		not specified	Uncertain significance (May 25, 2022)
12-130422455-A-T		not specified	Uncertain significance (Dec 12, 2023)
12-130424283-C-T			Likely benign (Dec 01, 2022)
12-130424361-C-T			Likely benign (Oct 01, 2022)
12-130428189-T-C		not specified	Uncertain significance (Feb 17, 2024)
12-130428198-G-A		not specified	Uncertain significance (May 17, 2023)
12-130428223-C-G		not specified	Uncertain significance (Dec 07, 2023)
12-130428225-T-C		not specified	Uncertain significance (May 09, 2023)
12-130428310-G-A		not specified	Uncertain significance (Dec 16, 2023)
12-130428330-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-130434753-C-G		not specified	Uncertain significance (Aug 13, 2021)
12-130434807-T-C		not specified	Uncertain significance (Oct 20, 2023)
12-130434879-A-G		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIMBP2	protein_coding	protein_coding	ENST00000261655	17	320145

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.678	0.322	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	562	658	0.853	0.0000439	6809
Missense in Polyphen		146	240.13	0.608		2516
Synonymous	-1.02	310	288	1.08	0.0000223	2130
Loss of Function	4.82	9	43.2	0.208	0.00000207	513

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000419
Ashkenazi Jewish	0.000815	0.000794
East Asian	0.000224	0.000217
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000280	0.000273
Middle Eastern	0.000224	0.000217
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the synaptic transmission as bifunctional linker that interacts simultaneously with RIMS1, RIMS2, CACNA1D and CACNA1B. {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.418
• rvis_EVS: -2.07
• rvis_percentile_EVS: 1.62

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.558
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rimbp2
• Phenotype: normal phenotype; 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)

Gene ontology

• Biological process: neuromuscular synaptic transmission;negative regulation of phosphatase activity
• Cellular component: plasma membrane;cell junction;synapse