SCAF1

SR-related CTD associated factor 1

Basic information

Region (hg38): 19:49642208-49658642

Links

ENSG00000126461 ∙ NCBI:58506 ∙ OMIM:617264 ∙ HGNC:30403 ∙ Uniprot:Q9H7N4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAF1 gene.

• Inborn genetic diseases (70 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAF1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	2	6
missense			68	4	2	74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	8	4

Variants in SCAF1

This is a list of pathogenic ClinVar variants found in the SCAF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-49645071-G-C			Benign (Jun 26, 2018)
19-49645079-G-A			Benign (May 21, 2018)
19-49645354-C-G		not specified	Uncertain significance (Aug 08, 2023)
19-49645388-A-G		not specified	Uncertain significance (Feb 28, 2023)
19-49645403-A-T		not specified	Uncertain significance (Jan 26, 2023)
19-49646556-G-T			Benign (Jun 26, 2018)
19-49646568-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-49646605-G-A		not specified	Likely benign (Dec 07, 2021)
19-49646616-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-49646765-A-G		not specified	Uncertain significance (Oct 17, 2023)
19-49646809-G-T		not specified	Uncertain significance (Mar 23, 2022)
19-49650880-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-49650907-G-C		not specified	Uncertain significance (Feb 17, 2023)
19-49650933-G-A			Likely benign (Apr 01, 2023)
19-49650959-C-A			Likely benign (Nov 01, 2022)
19-49651027-C-T		not specified	Uncertain significance (Apr 22, 2022)
19-49651033-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-49651041-C-T		not specified	Uncertain significance (Feb 07, 2023)
19-49651054-C-T		not specified	Uncertain significance (May 24, 2023)
19-49651059-C-A			Likely benign (Apr 01, 2023)
19-49651110-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-49651174-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-49651202-G-C			Likely benign (Feb 01, 2023)
19-49651236-G-T		not specified	Uncertain significance (Jan 19, 2022)
19-49651238-C-G		not specified	Likely benign (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAF1	protein_coding	protein_coding	ENST00000360565	10	16518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00181	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	579	682	0.849	0.0000489	8030
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.000113	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.149

Haploinsufficiency Scores

• pHI: 0.197
• hipred: Y
• hipred_score: 0.527
• ghis: 0.559

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.720

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scaf1

Gene ontology

• Biological process: transcription by RNA polymerase II;mRNA processing;RNA splicing
• Cellular component: nucleus
• Molecular function: RNA binding;protein domain specific binding;RNA polymerase II C-terminal domain binding