EPSTI1

epithelial stromal interaction 1

Basic information

Region (hg38): 13:42886387-42992271

Links

ENSG00000133106 ∙ NCBI:94240 ∙ OMIM:607441 ∙ HGNC:16465 ∙ Uniprot:Q96J88 ∙ 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 EPSTI1 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPSTI1 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			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	24	2	1

Variants in EPSTI1

This is a list of pathogenic ClinVar variants found in the EPSTI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-42888292-T-C		not specified	Likely benign (Jul 20, 2021)
13-42888300-C-T		not specified	Uncertain significance (Feb 27, 2023)
13-42888303-G-T		not specified	Likely benign (Sep 25, 2023)
13-42888312-C-G		not specified	Uncertain significance (Mar 29, 2023)
13-42888323-G-T		not specified	Uncertain significance (Apr 22, 2022)
13-42888333-G-A		not specified	Uncertain significance (Mar 07, 2024)
13-42888372-G-A		not specified	Uncertain significance (Dec 13, 2023)
13-42888375-T-C		not specified	Uncertain significance (May 17, 2023)
13-42888392-A-G		not specified	Uncertain significance (Mar 11, 2022)
13-42888395-G-A		not specified	Uncertain significance (Dec 13, 2021)
13-42888444-G-A		not specified	Uncertain significance (Feb 22, 2023)
13-42888467-G-A		not specified	Likely benign (Oct 05, 2022)
13-42889216-G-C		not specified	Uncertain significance (Dec 28, 2022)
13-42895107-C-T		not specified	Uncertain significance (Nov 12, 2021)
13-42900362-G-A		not specified	Uncertain significance (Nov 30, 2022)
13-42900371-C-G		not specified	Uncertain significance (Mar 29, 2023)
13-42917619-T-A		not specified	Uncertain significance (Oct 12, 2022)
13-42926374-A-C		not specified	Uncertain significance (Jun 06, 2023)
13-42953987-T-C		not specified	Uncertain significance (Dec 06, 2022)
13-42953995-T-A		not specified	Uncertain significance (May 04, 2023)
13-42963299-C-T		not specified	Uncertain significance (Oct 26, 2021)
13-42963323-A-G		not specified	Uncertain significance (May 30, 2023)
13-42964121-G-A		Malignant tumor of prostate	Uncertain significance (-)
13-42964136-C-T		not specified	Uncertain significance (May 27, 2022)
13-42964145-G-GA			Benign (Apr 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPSTI1	protein_coding	protein_coding	ENST00000313640	13	105884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.31e-25	0.0000185	125237	2	509	125748	0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.425	231	214	1.08	0.0000103	2687
Missense in Polyphen		50	53.363	0.93698		755
Synonymous	0.130	79	80.5	0.982	0.00000399	746
Loss of Function	-1.38	33	25.5	1.29	0.00000114	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000766	0.000761
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00105	0.00102
Middle Eastern	0.000766	0.000761
South Asian	0.0115	0.0108
Other	0.00165	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in M1 macrophage polarization and is required for the proper regulation of gene expression during M1 versus M2 macrophage differentiation (By similarity). Might play a role in RELA/p65 and STAT1 phosphorylation and nuclear localization upon activation of macrophages (By similarity). {ECO:0000250|UniProtKB:Q8VDI1}.

Recessive Scores

• pRec: 0.0744

Intolerance Scores

• loftool: 0.321
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.123
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Epsti1