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GeneBe

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

ENSG00000139218NCBI:9169OMIM:603668HGNC:10784Uniprot:Q99590AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCAF11 gene.

  • Inborn genetic diseases (49 variants)
  • not provided (3 variants)

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
clinvar
2
missense
46
clinvar
2
clinvar
48
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
1
Total 0 0 47 2 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)3158158
12-45922170-C-T not specified Uncertain significance (Oct 06, 2023)3158157
12-45922950-A-C not specified Uncertain significance (Mar 28, 2022)2231248
12-45922974-C-A not specified Uncertain significance (Apr 05, 2023)2533235
12-45923075-G-A not specified Likely benign (Dec 13, 2021)3158156
12-45923114-G-A not specified Uncertain significance (Sep 23, 2023)3158155
12-45923138-G-A not specified Uncertain significance (Jul 12, 2023)2611373
12-45924804-G-T not specified Uncertain significance (Aug 11, 2022)2306517
12-45924829-G-A not specified Uncertain significance (Oct 29, 2021)2219397
12-45924882-G-A not specified Uncertain significance (Mar 16, 2022)2278690
12-45924904-G-A not specified Uncertain significance (Feb 14, 2023)2483695
12-45924914-C-G not specified Uncertain significance (Jun 11, 2021)3158153
12-45924924-G-C not specified Uncertain significance (Jan 30, 2024)3158152
12-45924968-T-A not specified Uncertain significance (Oct 27, 2021)2257782
12-45925013-C-A not specified Uncertain significance (Mar 29, 2022)2327714
12-45925014-A-G not specified Uncertain significance (Aug 28, 2023)2600351
12-45925071-G-C not specified Uncertain significance (May 30, 2023)2525853
12-45926379-T-C not specified Uncertain significance (Jun 22, 2023)2605489
12-45926384-T-C not specified Uncertain significance (Jun 05, 2023)2508164
12-45926414-C-T not specified Uncertain significance (Jul 27, 2022)2217056
12-45926419-T-G not specified Uncertain significance (May 17, 2023)2523183
12-45926435-T-C not specified Uncertain significance (Apr 26, 2023)2540925
12-45926500-C-A not specified Uncertain significance (Oct 06, 2023)3158149
12-45926526-A-G not specified Uncertain significance (Nov 10, 2022)2325665
12-45926560-C-A not specified Uncertain significance (Dec 09, 2023)3158148

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCAF11protein_codingprotein_codingENST00000369367 1472990
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000003671257230241257470.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5386987390.9440.00003669640
Missense in Polyphen147191.580.76732292
Synonymous-0.5622692581.040.00001242736
Loss of Function6.56661.50.09760.00000333797

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001830.000182
Ashkenazi Jewish0.0001010.0000992
East Asian0.00005450.0000544
Finnish0.0001390.000139
European (Non-Finnish)0.0001240.000123
Middle Eastern0.00005450.0000544
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scaf11
Phenotype

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