RBM48

protein-coding

RNA binding motif protein 48, the group of RNA binding motif containing

Gene summary

Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C7orf64

MANE transcript

NM_032120.4

Inheritance

—

ClinVar variants

P:1U:71B:13

Top phenotype

Nephronophthisis

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr7:92,528,773-92,540,481

External References & Databases

Ensembl (ENSG00000127993)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 RBM48 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 53

not providedTotal: 35

NephronophthisisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032120.4. 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	5 clinvar	2 clinvar	8
missense		1 clinvar	64 clinvar	5 clinvar	1 clinvar	71
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	71	10	3	85

Highest pathogenic variant AF is 0.000017347644

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032120.4	RefSeq	NP_115496.2	5	MANE Select
ENST00000265732.10	Ensembl	ENSP00000265732.5	5	MANE Select
NM_001363366.1	RefSeq	NP_001350295.1	6	Standard
NM_001363367.1	RefSeq	NP_001350296.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265732
Coding exons: 5
Length: 9233
Individuals with no LoFs: 124744
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 124795
p: 0.000204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.322	188	201	0.936	0.0000103	2397
Missense (PolyPhen)		38	50.47	0.75293		612
Synonymous	0.157	71	72.7	0.977	0.00000383	691
Loss of Function	0.705	12	14.9	0.803	7.18e-7	206

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.000064	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00039	0.00034	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0986

Intolerance Scores

RVIS EVS: -0.27
RVIS percentile EVS: 34.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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