RBM22

Basic information

Region (hg38): 5:150690792-150701077

Links

ENSG00000086589

∙ NCBI:55696 ∙ OMIM:612430 ∙ HGNC:25503 ∙ Uniprot:Q9NW64 ∙ 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 RBM22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM22 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 clinvar	1
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in RBM22

This is a list of pathogenic ClinVar variants found in the RBM22 region.

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

Position	Phenotype	Significance	ClinVar
5-150691770-C-G	not specified	Uncertain significance (Dec 27, 2022)	2339612
5-150691843-G-C	not specified	Uncertain significance (Aug 20, 2023)	2619695
5-150691844-G-C	RBM22-related disorder	Benign (Jun 15, 2018)	773937
5-150691870-G-A	not specified	Uncertain significance (Jan 10, 2023)	2475083
5-150692940-T-C	not specified	Uncertain significance (May 27, 2022)	2291904
5-150692964-T-C	not specified	Uncertain significance (Nov 21, 2023)	3152256
5-150692969-G-A	not specified	Uncertain significance (Mar 04, 2024)	3152255
5-150692991-A-G	not specified	Uncertain significance (Jan 14, 2025)	3787524
5-150694152-C-T	not specified	Uncertain significance (Jun 11, 2024)	3313243
5-150694205-A-G	not specified	Uncertain significance (Jan 24, 2024)	3152258
5-150694208-G-A	not specified	Uncertain significance (Jun 23, 2023)	2596767
5-150694234-A-C	not specified	Uncertain significance (May 24, 2023)	2551281
5-150695594-T-C	not specified	Uncertain significance (Jun 16, 2024)	3313244
5-150695605-C-T	not specified	Uncertain significance (Mar 06, 2025)	3787525
5-150695698-T-G	not specified	Uncertain significance (Apr 27, 2023)	2541497
5-150696596-C-T	not specified	Uncertain significance (May 30, 2024)	3313242
5-150696701-G-T	not specified	Uncertain significance (Jun 02, 2023)	2555867
5-150696844-T-C	not specified	Uncertain significance (Nov 25, 2024)	2224164
5-150696868-C-T	not specified	Uncertain significance (Jan 31, 2024)	3152257
5-150700993-G-A	RBM22-related disorder	Likely benign (Feb 26, 2020)	3051146

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM22	protein_coding	protein_coding	ENST00000199814	11	10314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000535	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.16	104	242	0.429	0.0000130	2736
Missense in Polyphen		24	90.348	0.26564		977
Synonymous	1.58	63	81.1	0.777	0.00000391	822
Loss of Function	4.32	0	21.7	0.00	9.86e-7	273

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses. {ECO:0000269|PubMed:17045351, ECO:0000269|PubMed:21122810, ECO:0000269|PubMed:22246180}.;
Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.292
rvis_EVS: -0.41
rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

pHI: 0.390
hipred: Y
hipred_score: 0.783
ghis: 0.675

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rbm22
Phenotype

Zebrafish Information Network

Gene name: rbm22
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: flat

Gene ontology

Biological process: obsolete protein import into nucleus, translocation;spliceosomal snRNP assembly;mRNA splicing, via spliceosome;positive regulation of RNA splicing;cellular response to drug;positive regulation of protein import into nucleus;mRNA cis splicing, via spliceosome;positive regulation of protein export from nucleus
Cellular component: Prp19 complex;nucleus;nucleoplasm;cytoplasm;U2-type catalytic step 1 spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
Molecular function: RNA binding;protein binding;U6 snRNA binding;pre-mRNA binding;metal ion binding;calcium-dependent protein binding