SRFBP1

protein-coding

serum response factor binding protein 1

Gene summary

Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA. Predicted to be located in perinuclear region of cytoplasm. Predicted to be part of 90S preribosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152546.3

Inheritance

—

ClinVar variants

U:71B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr5:121,961,975-122,075,570

External References & Databases

Ensembl (ENSG00000151304)

Transcript & Mutation Effects

hg38 • Region Span ~113.6 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 SRFBP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 69

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152546.3. 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						0
missense			69 clinvar	2 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	71	2	0	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152546.3	RefSeq	NP_689759.2	8	MANE Select
ENST00000339397.5	Ensembl	ENSP00000341324.4	8	MANE Select
ENST00000919756.1	Ensembl	ENSP00000589815.1	6	Standard
ENST00000919756.2	Ensembl	ENSP00000589815.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

maturation of SSU-rRNA

Molecular Function

RNA binding

Cellular Component

nucleus
90S preribosome
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339397
Coding exons: 8
Length: 113610
Individuals with no LoFs: 124709
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 124790
p: 0.000325

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.62	276	210	1.31	0.0000101	2813
Missense (PolyPhen)		73	60.429	1.208		815
Synonymous	-1.73	92	73.1	1.26	0.00000342	785
Loss of Function	0.623	19	22.2	0.857	0.00000135	277

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00060	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00028	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00044	0.00043	rare
South Asian	0.00016	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in regulating transcriptional activation of cardiac genes during the aging process. May play a role in biosynthesis and/or processing of SLC2A4 in adipose cells (By similarity). {ECO:0000250|UniProtKB:Q9CZ91}.;

Recessive Scores

pRec: 0.137

Intolerance Scores

LoFtool: 0.247
RVIS EVS: 1.02
RVIS percentile EVS: 91.02

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.275

Gene Damage Prediction

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