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

ENSG00000153914 ∙ NCBI:140890 ∙ OMIM:609268 ∙ HGNC:17882 ∙ Uniprot:Q8WXA9 ∙ 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 SREK1 gene.

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.

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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in SREK1

This is a list of pathogenic ClinVar variants found in the SREK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-66144386-G-C		not specified	Uncertain significance (Dec 31, 2024)
5-66144419-C-G		not specified	Uncertain significance (Jan 09, 2025)
5-66144425-C-T		not specified	Uncertain significance (Jan 19, 2024)
5-66144483-G-A		not specified	Uncertain significance (Dec 11, 2024)
5-66144515-G-A		not specified	Uncertain significance (Dec 12, 2024)
5-66144522-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-66159317-C-T		not specified	Uncertain significance (Jul 13, 2021)
5-66159320-A-G		not specified	Uncertain significance (Aug 21, 2024)
5-66162118-T-A		not specified	Uncertain significance (Feb 05, 2024)
5-66162418-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-66164789-G-A		not specified	Uncertain significance (Apr 05, 2023)
5-66164818-T-A		not specified	Uncertain significance (Mar 04, 2024)
5-66164822-G-A		not specified	Uncertain significance (Jul 14, 2023)
5-66164827-C-G		not specified	Uncertain significance (Jul 05, 2024)
5-66164886-A-C		not specified	Uncertain significance (Jul 30, 2024)
5-66170073-C-T		not specified	Uncertain significance (Jan 21, 2025)
5-66170113-A-T		not specified	Uncertain significance (May 10, 2024)
5-66170121-C-T		not specified	Uncertain significance (Dec 17, 2023)
5-66170142-C-T		not specified	Uncertain significance (Mar 20, 2024)
5-66170157-C-T		not specified	Uncertain significance (Apr 23, 2024)
5-66170676-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-66170694-C-T		not specified	Uncertain significance (Dec 16, 2024)
5-66170698-G-A		not specified	Uncertain significance (Mar 19, 2024)
5-66170712-C-T		not specified	Uncertain significance (Jan 23, 2025)
5-66170713-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SREK1	protein_coding	protein_coding	ENST00000334121	12	43645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.915	0.0852	125726	0	15	125741	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	228	346	0.658	0.0000198	4070
Missense in Polyphen		25	72.279	0.34588		877
Synonymous	-0.0643	118	117	1.01	0.00000607	1180
Loss of Function	4.22	5	29.9	0.167	0.00000182	389

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000209	0.000198
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000909	0.0000879
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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

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

Mouse Genome Informatics

• Gene name: Srek1

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