SCAF1

protein-coding

SR-related CTD associated factor 1

Gene summary

Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021228.3

Inheritance

—

ClinVar variants

U:262B:14

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr19:49,642,209-49,658,642

External References & Databases

Ensembl (ENSG00000126461)

Transcript & Mutation Effects

hg38 • Region Span ~16.4 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 SCAF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 254

not providedTotal: 16

EBV-positive nodal T- and NK-cell lymphomaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021228.3. 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			4 clinvar	5 clinvar	2 clinvar	11
missense			254 clinvar	5 clinvar	2 clinvar	261
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	262	10	4	276

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021228.3	RefSeq	NP_067051.2	10	MANE Select
ENST00000360565.8	Ensembl	ENSP00000353769.2	10	MANE Select
ENST00000595242.3	Ensembl	ENSP00000472276.1	4	Standard
ENST00000598359.5	Ensembl	ENSP00000473210.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription by RNA polymerase II
mRNA processing
RNA splicing

Molecular Function

RNA binding
protein domain specific binding
RNA polymerase II C-terminal domain binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360565
Coding exons: 10
Length: 16518
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125744
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.40	579	682	0.849	0.0000489	8030
Missense (PolyPhen)		21	48.561	0.43245		506
Synonymous	-2.45	366	311	1.18	0.0000230	2901
Loss of Function	4.95	4	36.1	0.111	0.00000209	471

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function in pre-mRNA splicing. {ECO:0000250}.;

Recessive Scores

pRec: 0.149

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.720

Gene Damage Prediction

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