SCAF11

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

Basic information

Region (hg38): 12:45919130-45992120

Previous symbols: [ "SFRS2IP", "SRSF2IP" ]

Links

ENSG00000139218 ∙ NCBI:9169 ∙ OMIM:603668 ∙ HGNC:10784 ∙ Uniprot:Q99590 ∙ 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 SCAF11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAF11 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					2	2
missense			67	7		74
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	69	7	2

Variants in SCAF11

This is a list of pathogenic ClinVar variants found in the SCAF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-45922062-T-C		not specified	Uncertain significance (Oct 16, 2023)
12-45922170-C-T		not specified	Uncertain significance (Oct 06, 2023)
12-45922950-A-C		not specified	Uncertain significance (Mar 28, 2022)
12-45922974-C-A		not specified	Uncertain significance (Apr 05, 2023)
12-45923075-G-A		not specified	Likely benign (Dec 13, 2021)
12-45923114-G-A		not specified	Uncertain significance (Sep 23, 2023)
12-45923138-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-45924804-G-T		not specified	Uncertain significance (Aug 11, 2022)
12-45924829-G-A		not specified	Uncertain significance (Oct 29, 2021)
12-45924882-G-A		not specified	Uncertain significance (Mar 16, 2022)
12-45924904-G-A		not specified	Uncertain significance (Feb 14, 2023)
12-45924914-C-G		not specified	Uncertain significance (Jun 11, 2021)
12-45924924-G-C		not specified	Uncertain significance (Jan 30, 2024)
12-45924968-T-A		not specified	Uncertain significance (Oct 27, 2021)
12-45925013-C-A		not specified	Uncertain significance (Mar 29, 2022)
12-45925014-A-G		not specified	Uncertain significance (Aug 28, 2023)
12-45925071-G-C		not specified	Uncertain significance (May 30, 2023)
12-45926379-T-C		not specified	Uncertain significance (Jun 22, 2023)
12-45926384-T-C		not specified	Uncertain significance (Jun 05, 2023)
12-45926414-C-T		not specified	Uncertain significance (Jul 27, 2022)
12-45926419-T-G		not specified	Uncertain significance (May 17, 2023)
12-45926435-T-C		not specified	Uncertain significance (Apr 26, 2023)
12-45926500-C-A		not specified	Uncertain significance (Oct 06, 2023)
12-45926526-A-G		not specified	Uncertain significance (Nov 10, 2022)
12-45926560-C-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAF11	protein_coding	protein_coding	ENST00000369367	14	72990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000367	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.538	698	739	0.944	0.0000366	9640
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in pre-mRNA alternative splicing by regulating spliceosome assembly. {ECO:0000269|PubMed:9447963}.
• Pathway: Apoptosis;Apoptotic Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.78

Haploinsufficiency Scores

• pHI: 0.156
• hipred: Y
• hipred_score: 0.542
• ghis: 0.614

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scaf11

Gene ontology

• Biological process: spliceosomal complex assembly;RNA splicing, via transesterification reactions;mRNA processing;RNA splicing
• Cellular component: nucleus;nucleoplasm;nucleolus;nuclear body
• Molecular function: RNA binding;protein binding;metal ion binding