RBMS3

protein-coding

RNA binding motif single stranded interacting protein 3, the group of RNA binding motif containing

Gene summary

This gene encodes an RNA-binding protein that belongs to the c-myc gene single-strand binding protein family. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. These proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. The encoded protein was isolated by virtue of its binding to an upstream element of the alpha2(I) collagen promoter. The observation that this protein localizes mostly in the cytoplasm suggests that it may be involved in a cytoplasmic function such as controlling RNA metabolism, rather than transcription. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

MANE transcript

NM_001003793.3

Inheritance

—

ClinVar variants

U:57B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr3:28,574,791-30,010,391

External References & Databases

Ensembl (ENSG00000144642)

Transcript & Mutation Effects

hg38 • Region Span ~1,435.6 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 RBMS3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001003793.3. 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	2 clinvar	3 clinvar	6
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	4	3	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 70 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001003793.3	RefSeq	NP_001003793.1	15	MANE Select
ENST00000383767.7	Ensembl	ENSP00000373277.2	15	MANE Select
NM_001003792.3	RefSeq	NP_001003792.1	14	Standard
NM_001177711.2	RefSeq	NP_001171182.1	14	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rbms3	Danio rerio	Structure: chondrocranium cartilage Quality: malformed abnormal

Gene / Model

Organism

Observed Phenotype

rbms3

Danio rerio

Structure: chondrocranium cartilage

Quality: malformed

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

defense response to tumor cell
positive regulation of gene expression
negative regulation of gene expression
positive regulation of translation
negative regulation of canonical Wnt signaling pathway

Molecular Function

RNA binding
mRNA 3'-UTR binding
poly(A) binding
poly(U) RNA binding
mRNA 3'-UTR AU-rich region binding

Cellular Component

nucleus
cytoplasm
cytosol
ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383767
Coding exons: 15
Length: 729414
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125746
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	185	241	0.769	0.0000118	2864
Missense (PolyPhen)		76	117.99	0.64414		1417
Synonymous	0.751	76	84.8	0.896	0.00000476	805
Loss of Function	3.78	7	28.9	0.242	0.00000147	317

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.0010	notable
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds poly(A) and poly(U) oligoribonucleotides. {ECO:0000269|PubMed:10675610}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.749
RVIS EVS: -0.6
RVIS percentile EVS: 17.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.427

Gene Damage Prediction

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