RBM22

protein-coding

Gene summary

This gene encodes an RNA binding protein. The encoded protein may play a role in cell division and may be involved in pre-mRNA splicing. Related pseudogenes exist on chromosomes 6, 7, 9, 13, 16, 18, and X. [provided by RefSeq, Mar 2009]

MANE transcript

NM_018047.3

Inheritance

—

ClinVar variants

U:37B:1

Top phenotype

RBM22-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr5:150,690,792-150,701,077

External References & Databases

Ensembl (ENSG00000086589)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RBM22 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

RBM22-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018047.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			35 clinvar			35
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	37	0	1	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018047.3	RefSeq	NP_060517.1	11	MANE Select
ENST00000199814.9	Ensembl	ENSP00000199814.4	11	MANE Select
ENST00000447771.6	Ensembl	ENSP00000412118.2	10	Standard
ENST00000447771.7	Ensembl	ENSP00000412118.2	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rbm22	Danio rerio	Structure: head Quality: flat abnormal

Gene / Model

Organism

Observed Phenotype

rbm22

Danio rerio

Structure: head

Quality: flat

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

obsolete protein import into nucleus, translocation
spliceosomal snRNP assembly
mRNA splicing, via spliceosome
positive regulation of RNA splicing
cellular response to drug

Molecular Function

RNA binding
protein binding
U6 snRNA binding
pre-mRNA binding
metal ion binding

Cellular Component

Prp19 complex
nucleus
nucleoplasm
cytoplasm
U2-type catalytic step 1 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000199814
Coding exons: 11
Length: 10314
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.16	104	242	0.429	0.0000130	2736
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.292
RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.793

Gene Damage Prediction

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