SCAF11

protein-coding

SR-related CTD associated factor 11, the group of Ring finger proteins

Gene summary

Enables RNA binding activity. Involved in spliceosomal complex assembly. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SFRS2IP
SRSF2IP

MANE transcript

NM_004719.3

Inheritance

—

ClinVar variants

U:179B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr12:45,919,131-45,992,120

External References & Databases

Ensembl (ENSG00000139218)

Transcript & Mutation Effects

hg38 • Region Span ~73.0 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 SCAF11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 181

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004719.3. 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			3 clinvar		3 clinvar	6
missense			170 clinvar	13 clinvar		183
nonsense			1 clinvar			1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	179	13	3	195

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004719.3	RefSeq	NP_004710.2	14	MANE Select
ENST00000369367.8	Ensembl	ENSP00000358374.3	14	MANE Select
ENST00000266589.10	Ensembl	ENSP00000266589.6	5	Standard
ENST00000395453.2	Ensembl	ENSP00000378839.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Apoptosis
Apoptotic Signaling Pathway

Biological Process

spliceosomal complex assembly
RNA splicing, via transesterification reactions
mRNA processing
RNA splicing

Molecular Function

RNA binding
protein binding
metal ion binding

Cellular Component

nucleus
nucleoplasm
nucleolus
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369367
Coding exons: 14
Length: 72990
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125747
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.538	698	739	0.944	0.0000366	9640
Missense (PolyPhen)		147	191.58	0.7673		2292
Synonymous	-0.562	269	258	1.04	0.0000124	2736
Loss of Function	6.56	6	61.5	0.0976	0.00000333	797

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in pre-mRNA alternative splicing by regulating spliceosome assembly. {ECO:0000269|PubMed:9447963}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

RVIS EVS: -0.21
RVIS percentile EVS: 37.78

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
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