SREK1IP1

SREK1 interacting protein 1

Basic information

Region (hg38): 5:64718147-64768691

Previous symbols: [ "SFRS12IP1" ]

Links

ENSG00000153006 ∙ NCBI:285672 ∙ ∙ HGNC:26716 ∙ Uniprot:Q8N9Q2 ∙ 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 SREK1IP1 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SREK1IP1 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in SREK1IP1

This is a list of pathogenic ClinVar variants found in the SREK1IP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-64724517-T-A		not specified	Uncertain significance (Aug 09, 2021)
5-64728179-C-T		not specified	Uncertain significance (Feb 15, 2023)
5-64741141-C-T		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SREK1IP1	protein_coding	protein_coding	ENST00000513458	5	50542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.387	0.604	125699	0	20	125719	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.624	52	66.3	0.784	0.00000317	1030
Missense in Polyphen		11	15.657	0.70258		221
Synonymous	-0.791	26	21.4	1.22	0.00000100	220
Loss of Function	2.20	2	9.18	0.218	5.63e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000529	0.000502
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000353	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible splicing regulator involved in the control of cellular survival.

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.231
• hipred: N
• hipred_score: 0.367
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• 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: Srek1ip1

Gene ontology

• Biological process: mRNA processing;RNA splicing
• Molecular function: nucleic acid binding;protein binding;zinc ion binding