SFSWAP

protein-coding

splicing factor SWAP

Gene summary

This gene encodes a human homolog of Drosophila splicing regulatory protein. This gene autoregulates its expression by control of splicing of its first two introns. In addition, it also regulates the splicing of fibronectin and CD45 genes. Two transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012]

Previous symbols:

SFRS8

MANE transcript

NM_004592.4

Inheritance

—

ClinVar variants

U:135B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr12:131,711,081-131,799,738

External References & Databases

Ensembl (ENSG00000061936)

Transcript & Mutation Effects

hg38 • Region Span ~88.7 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 SFSWAP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 127

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004592.4. 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			2 clinvar	5 clinvar		7
missense			128 clinvar	9 clinvar		137
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	135	14	0	149

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004592.4	RefSeq	NP_004583.2	18	MANE Select
ENST00000261674.9	Ensembl	ENSP00000261674.4	18	MANE Select
NM_001261411.2	RefSeq	NP_001248340.1	19	Standard
ENST00000537164.1	Ensembl	ENSP00000439957.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA Processing

Biological Process

alternative mRNA splicing, via spliceosome
mRNA 5'-splice site recognition
negative regulation of mRNA splicing, via spliceosome

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000541286
Coding exons: 19
Length: 88657
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125746
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.80	439	638	0.688	0.0000412	6480
Missense (PolyPhen)		102	208.31	0.48965		2193
Synonymous	-0.546	286	275	1.04	0.0000201	2022
Loss of Function	5.89	3	46.2	0.0649	0.00000220	591

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	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role as an alternative splicing regulator. Regulate its own expression at the level of RNA processing. Also regulates the splicing of fibronectin and CD45 genes. May act, at least in part, by interaction with other R/S-containing splicing factors. Represses the splicing of MAPT/Tau exon 10. {ECO:0000269|PubMed:8940107}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

RVIS EVS: -0.96
RVIS percentile EVS: 9

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