EVI5L

ecotropic viral integration site 5 like

Basic information

Region (hg38): 19:7830218-7864976

Links

ENSG00000142459 ∙ NCBI:115704 ∙ ∙ HGNC:30464 ∙ Uniprot:Q96CN4 ∙ 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 EVI5L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVI5L 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in EVI5L

This is a list of pathogenic ClinVar variants found in the EVI5L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7846610-C-T		not specified	Uncertain significance (Jun 29, 2023)
19-7847745-G-A		not specified	Uncertain significance (May 13, 2024)
19-7847760-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-7847848-A-G		not specified	Uncertain significance (Nov 27, 2023)
19-7847869-G-A		not specified	Uncertain significance (May 27, 2022)
19-7848964-T-C		not specified	Uncertain significance (Mar 20, 2024)
19-7848984-G-T		not specified	Uncertain significance (Sep 16, 2021)
19-7849057-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-7851465-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-7851542-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-7851545-G-A		not specified	Uncertain significance (Jun 21, 2023)
19-7851700-G-C		not specified	Uncertain significance (Jul 07, 2024)
19-7858270-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-7860588-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-7860594-C-T		not specified	Uncertain significance (Jun 01, 2022)
19-7860606-G-A		not specified	Uncertain significance (Jul 11, 2023)
19-7860634-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-7860675-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-7860678-G-A		not specified	Uncertain significance (Sep 14, 2023)
19-7861980-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-7862140-G-C		not specified	Uncertain significance (Oct 06, 2024)
19-7862199-G-A		not specified	Uncertain significance (Mar 12, 2024)
19-7862240-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-7862401-G-T		not specified	Uncertain significance (Feb 15, 2023)
19-7862436-G-A		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVI5L	protein_coding	protein_coding	ENST00000538904	19	34744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000153	125735	0	2	125737	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.23	217	477	0.455	0.0000307	5156
Missense in Polyphen		74	182.66	0.40513		1994
Synonymous	2.53	173	221	0.783	0.0000153	1563
Loss of Function	5.49	4	42.7	0.0937	0.00000195	497

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a GTPase-activating protein (GAP) with a broad specificity. {ECO:0000269|PubMed:16923123}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.231
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.534
• hipred: Y
• hipred_score: 0.610
• ghis: 0.699

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evi5l

Gene ontology

• Biological process: intracellular protein transport;positive regulation of GTPase activity;activation of GTPase activity;negative regulation of cilium assembly
• Cellular component: cell
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding