EBPL

EBP like

Basic information

Region (hg38): 13:49660673-49691486

Links

ENSG00000123179 ∙ NCBI:84650 ∙ OMIM:617335 ∙ HGNC:18061 ∙ Uniprot:Q9BY08 ∙ 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 EBPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBPL 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in EBPL

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

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

Position	Type	Phenotype	Significance	ClinVar
13-49661060-C-A		not specified	Uncertain significance (Dec 19, 2022)
13-49661063-A-T		not specified	Uncertain significance (Dec 16, 2023)
13-49661122-T-C		not specified	Uncertain significance (Nov 22, 2022)
13-49661177-C-G		not specified	Uncertain significance (Jun 29, 2023)
13-49661177-C-T		not specified	Uncertain significance (May 23, 2024)
13-49661183-C-T		not specified	Uncertain significance (Jun 10, 2024)
13-49663058-G-A		not specified	Uncertain significance (Apr 20, 2024)
13-49663078-A-G		not specified	Uncertain significance (Dec 27, 2023)
13-49663111-T-C		not specified	Uncertain significance (May 08, 2024)
13-49663118-C-A		not specified	Uncertain significance (Sep 01, 2021)
13-49663118-C-T		not specified	Uncertain significance (Sep 26, 2022)
13-49663171-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-49691295-G-A		not specified	Uncertain significance (Jul 12, 2023)
13-49691301-C-A		not specified	Uncertain significance (Mar 21, 2023)
13-49691318-T-C		not specified	Likely benign (Feb 23, 2023)
13-49691346-C-T		not specified	Uncertain significance (May 31, 2023)
13-49691357-G-T		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EBPL	protein_coding	protein_coding	ENST00000242827	4	30753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000782	0.538	125729	1	18	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	69	97.4	0.708	0.00000495	1282
Missense in Polyphen		31	42.271	0.73336		530
Synonymous	0.0598	43	43.5	0.988	0.00000247	422
Loss of Function	0.559	7	8.79	0.796	3.75e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000232	0.000232
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Does not possess sterol isomerase activity and does not bind sigma ligands. {ECO:0000269|PubMed:12760743}.

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• loftool: 0.446
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.0503
• hipred: N
• hipred_score: 0.170
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ebpl

Gene ontology

• Biological process: sterol metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: cholestenol delta-isomerase activity