RBM12B

protein-coding

RNA binding motif protein 12B, the group of RNA binding motif containing

Gene summary

Enables RNA binding activity. Predicted to be involved in regulation of RNA splicing. Predicted to be part of ribonucleoprotein complex. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001377960.1

Inheritance

—

ClinVar variants

U:150B:11

Top phenotype

Myoepithelial tumor

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr8:93,728,155-93,741,017

External References & Databases

Ensembl (ENSG00000183808)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 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 RBM12B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 159

not providedTotal: 1

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001377960.1. 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			150 clinvar	10 clinvar		160
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	150	11	0	161

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001377960.1	RefSeq	NP_001364889.1	1	MANE Select
ENST00000520560.6	Ensembl	ENSP00000429807.2	1	MANE Select
NM_001377961.1	RefSeq	NP_001364890.1	1	Standard
NM_001377962.1	RefSeq	NP_001364891.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399300
Coding exons: 1
Length: 11662
Individuals with no LoFs: 124740
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 124794
p: 0.000216

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.859	514	572	0.899	0.0000346	6646
Missense (PolyPhen)		179	248.97	0.71897		2891
Synonymous	-2.14	235	197	1.19	0.0000104	1933
Loss of Function	3.55	10	31.5	0.318	0.00000224	370

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00018	rare
South Asian	0.0014	0.00075	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.453
RVIS EVS: -0.53
RVIS percentile EVS: 20.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.765

Gene Damage Prediction

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