RBM7

protein-coding

RNA binding motif protein 7, the group of RNA binding motif containing|Nuclear exosome targeting complex

Gene summary

Enables 14-3-3 protein binding activity; pre-mRNA intronic binding activity; and snRNA binding activity. Involved in snRNA catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001286045.2

Inheritance

ClinVar variants

U:41

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr11:114,400,030-114,414,203

External References & Databases

Ensembl (ENSG00000076053)

Transcript & Mutation Effects

hg38 • Region Span ~14.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spinal muscular atrophyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0001516

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RBM7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286045.2. 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			40 clinvar			40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	41	0	0	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286045.2	RefSeq	NP_001272974.1	5	MANE Select
ENST00000375490.10	Ensembl	ENSP00000364639.5	5	MANE Select
NM_001286046.2	RefSeq	NP_001272975.1	2	Standard
NM_001286047.2	RefSeq	NP_001272976.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rbm7	Danio rerio	Structure: motor neuron Quality: branchiness abnormal

Gene / Model

Organism

Observed Phenotype

rbm7

Danio rerio

Structure: motor neuron

Quality: branchiness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of alternative mRNA splicing, via spliceosome
meiotic cell cycle

Molecular Function

RNA binding
single-stranded RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000540163
Coding exons: 5
Length: 14174
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125745
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.825	118	146	0.808	0.00000727	1752
Missense (PolyPhen)		17	34.903	0.48706		466
Synonymous	-0.380	53	49.6	1.07	0.00000235	481
Loss of Function	2.68	2	12.0	0.167	5.06e-7	154

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)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters (PubMed:27871484). Possible involved in germ cell RNA processing and meiosis (Probable). {ECO:0000269|PubMed:27871484, ECO:0000305|PubMed:12634307}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.386
RVIS EVS: -0.23
RVIS percentile EVS: 36.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.970

Gene Damage Prediction

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