SF1

splicing factor 1, the group of Zinc fingers CCHC-type|Spliceosomal A complex|Spliceosomal E complex

Basic information

Region (hg38): 11:64764606-64778786

Previous symbols: [ "ZNF162" ]

Links

ENSG00000168066 ∙ NCBI:7536 ∙ OMIM:601516 ∙ HGNC:12950 ∙ Uniprot:Q15637 ∙ 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 SF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SF1 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						0
missense			37	4		41
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	37	4	0

Variants in SF1

This is a list of pathogenic ClinVar variants found in the SF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64765470-A-G		not specified	Uncertain significance (Jun 11, 2021)
11-64765479-A-T		not specified	Uncertain significance (Nov 09, 2021)
11-64765486-T-C		not specified	Uncertain significance (May 11, 2022)
11-64765505-C-T		not specified	Likely benign (Feb 27, 2024)
11-64766916-G-A		not specified	Likely benign (May 15, 2024)
11-64767042-C-T		not specified	Likely benign (Dec 27, 2023)
11-64767043-G-A		not specified	Uncertain significance (May 24, 2023)
11-64767045-C-T		not specified	Likely benign (Dec 17, 2023)
11-64767053-T-A		not specified	Uncertain significance (May 26, 2024)
11-64767066-T-C		not specified	Likely benign (Oct 20, 2023)
11-64767230-G-A		not specified	Uncertain significance (May 09, 2022)
11-64767577-G-C		not specified	Uncertain significance (May 23, 2023)
11-64767727-T-C		not specified	Uncertain significance (Aug 17, 2021)
11-64767798-C-A		not specified	Uncertain significance (Aug 17, 2021)
11-64767814-G-A		not specified	Uncertain significance (Sep 26, 2023)
11-64768129-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-64768251-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-64769083-T-C		not specified	Uncertain significance (Jan 22, 2024)
11-64770347-G-A		not specified	Uncertain significance (Jan 24, 2024)
11-64773444-AG-A		Neurodevelopmental disorder	Likely pathogenic (May 04, 2021)
11-64776521-C-A		not specified	Uncertain significance (Nov 21, 2023)
11-64776534-G-A		not specified	Uncertain significance (Oct 16, 2023)
11-64778004-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-64778010-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-64778013-T-C		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SF1	protein_coding	protein_coding	ENST00000377387	13	14181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000569	120659	0	1	120660	0.00000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.62	151	338	0.446	0.0000202	4316
Missense in Polyphen		16	108.73	0.14716		1186
Synonymous	-2.27	152	120	1.26	0.00000716	1456
Loss of Function	4.54	1	25.9	0.0386	0.00000133	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000478	0.0000478
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. May act as transcription repressor. {ECO:0000269|PubMed:10449420, ECO:0000269|PubMed:8752089, ECO:0000269|PubMed:9660765}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;AndrogenReceptor;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.0867

Intolerance Scores

• loftool: 0.0225
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.65

Haploinsufficiency Scores

• pHI: 0.354
• hipred: Y
• hipred_score: 0.831
• ghis: 0.612

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sf1
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Zebrafish Information Network

• Gene name: sf1
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: spliceosomal complex assembly;mRNA 3'-splice site recognition;mRNA splicing, via spliceosome;male sex determination;nuclear body organization;Leydig cell differentiation;negative regulation of smooth muscle cell proliferation;regulation of steroid biosynthetic process;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;ribosome;nuclear body
• Molecular function: transcription corepressor activity;RNA binding;protein binding;zinc ion binding;identical protein binding;pre-mRNA branch point binding