SREK1

splicing regulatory glutamic acid and lysine rich protein 1, the group of RNA binding motif containing

Basic information

Region (hg38): 5:66139971-66183615

Previous symbols: [ "SFRS12" ]

Links

ENSG00000153914NCBI:140890OMIM:609268HGNC:17882Uniprot:Q8WXA9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SREK1 gene.

  • not_specified (68 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SREK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001077199.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
67
clinvar
1
clinvar
68
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 67 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SREK1protein_codingprotein_codingENST00000334121 1243645
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9150.08521257260151257410.0000596
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.262283460.6580.00001984070
Missense in Polyphen2572.2790.34588877
Synonymous-0.06431181171.010.000006071180
Loss of Function4.22529.90.1670.00000182389

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.0002090.000198
East Asian0.0001100.000109
Finnish0.00004620.0000462
European (Non-Finnish)0.00009090.0000879
Middle Eastern0.0001100.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3 (By similarity). {ECO:0000250}.;
Pathway
mRNA Processing (Consensus)

Recessive Scores

pRec
0.0940

Intolerance Scores

loftool
rvis_EVS
-0.29
rvis_percentile_EVS
33.2

Haploinsufficiency Scores

pHI
0.520
hipred
Y
hipred_score
0.693
ghis
0.634

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
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
Srek1
Phenotype

Gene ontology

Biological process
regulation of alternative mRNA splicing, via spliceosome;mRNA processing;RNA splicing
Cellular component
nucleoplasm;spliceosomal complex;nuclear speck
Molecular function
RNA binding;protein binding