RBM46

protein-coding

RNA binding motif protein 46, the group of RNA binding motif containing

Gene summary

Predicted to enable mRNA binding activity. Predicted to be involved in several processes, including cell cycle switching, mitotic to meiotic cell cycle; meiotic nuclear division; and spermatid differentiation. Predicted to act upstream of or within mRNA stabilization and trophectodermal cell differentiation. Predicted to be located in cytoplasm. Predicted to be part of apolipoprotein B mRNA editing enzyme complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144979.5

Inheritance

—

ClinVar variants

U:44

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr4:154,781,213-154,828,813

External References & Databases

Ensembl (ENSG00000151962)

Transcript & Mutation Effects

hg38 • Region Span ~47.6 kb

Loading mutation effect viewer...

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 RBM46 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144979.5. 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						0
missense			44 clinvar			44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	0	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144979.5	RefSeq	NP_659416.1	4	MANE Select
ENST00000281722.8	Ensembl	ENSP00000281722.3	4	MANE Select
NM_001277171.2	RefSeq	NP_001264100.1	4	Standard
NM_001277173.2	RefSeq	NP_001264102.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

trophectodermal cell differentiation
mRNA stabilization

Molecular Function

RNA binding
mRNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281722
Coding exons: 4
Length: 47601
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125711
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.10	178	276	0.644	0.0000133	3506
Missense (PolyPhen)		18	97.52	0.18458		1235
Synonymous	0.419	85	90.1	0.944	0.00000421	1014
Loss of Function	3.18	4	18.9	0.212	0.00000114	256

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.0019	0.0019	notable
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.144

Intolerance Scores

LoFtool: 0.439
RVIS EVS: -0.43
RVIS percentile EVS: 25.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.138

Gene Damage Prediction

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