SRSF4

protein-coding

serine and arginine rich splicing factor 4, the group of RNA binding motif containing|Serine and arginine rich splicing factors

Gene summary

Enables RNA binding activity. Involved in negative regulation of mRNA splicing, via spliceosome. Located in nuclear speck. Biomarker of Down syndrome; acute myeloid leukemia; clear cell renal cell carcinoma; and colon adenocarcinoma. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SFRS4

MANE transcript

NM_005626.5

Inheritance

—

ClinVar variants

U:52B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr1:29,147,743-29,181,900

External References & Databases

Ensembl (ENSG00000116350)

Transcript & Mutation Effects

hg38 • Region Span ~34.2 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 SRSF4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 51

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005626.5. 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			50 clinvar	3 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	52	3	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005626.5	RefSeq	NP_005617.2	6	MANE Select
ENST00000373795.7	Ensembl	ENSP00000362900.4	6	MANE Select
ENST00000466448.4	Ensembl	ENSP00000485813.1	5	Standard
ENST00000605204.1	Ensembl	ENSP00000473728.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
Herpes simplex infection - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
RNA Polymerase II Transcription

Biological Process

RNA splicing, via transesterification reactions
regulation of alternative mRNA splicing, via spliceosome
mRNA splicing, via spliceosome
mRNA processing
RNA export from nucleus

Molecular Function

RNA binding
protein binding
sequence-specific mRNA binding

Cellular Component

nucleus
nucleoplasm
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373795
Coding exons: 6
Length: 34245
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125747
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.40	205	327	0.627	0.0000223	3240
Missense (PolyPhen)		8	51.374	0.15572		535
Synonymous	-0.768	118	108	1.09	0.00000553	958
Loss of Function	3.81	4	24.2	0.165	0.00000185	253

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000067	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000070	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in alternative splice site selection during pre-mRNA splicing. Represses the splicing of MAPT/Tau exon 10. {ECO:0000269|PubMed:15009664}.;

Recessive Scores

pRec: 0.129

Intolerance Scores

RVIS EVS: 0.06
RVIS percentile EVS: 58.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High