EVI5

ecotropic viral integration site 5

Basic information

Region (hg38): 1:92508696-92792404

Links

ENSG00000067208 ∙ NCBI:7813 ∙ OMIM:602942 ∙ HGNC:3501 ∙ Uniprot:O60447 ∙ 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 EVI5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVI5 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				1	3	4
missense			47	2	2	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	3	5

Variants in EVI5

This is a list of pathogenic ClinVar variants found in the EVI5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-92513722-C-T			Likely benign (Mar 29, 2018)
1-92513741-C-T		not specified	Uncertain significance (Sep 14, 2022)
1-92513759-T-A		not specified	Uncertain significance (Sep 01, 2021)
1-92513797-A-G		not specified	Benign (Mar 29, 2016)
1-92513808-C-T		not specified	Likely benign (Oct 07, 2022)
1-92513846-T-C		not specified	Uncertain significance (Aug 02, 2021)
1-92513910-T-C		not specified	Uncertain significance (May 24, 2023)
1-92513963-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-92563658-G-A		not specified	Uncertain significance (May 25, 2023)
1-92563667-T-C		not specified	Uncertain significance (Mar 30, 2024)
1-92563718-T-G		not specified	Uncertain significance (Jan 09, 2023)
1-92605315-C-G		not specified	Uncertain significance (Mar 26, 2024)
1-92607606-C-T		not specified	Uncertain significance (Nov 27, 2023)
1-92607627-G-C		not specified	Uncertain significance (Jan 03, 2024)
1-92607671-C-A		not specified	Benign (Mar 29, 2016)
1-92607683-C-T			Benign (Mar 29, 2018)
1-92607696-G-A		not specified	Uncertain significance (Feb 17, 2024)
1-92607702-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-92607727-T-C		not specified	Uncertain significance (Sep 29, 2022)
1-92624219-T-C		not specified	Uncertain significance (May 18, 2023)
1-92624246-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-92624266-T-C		not specified	Benign (Mar 29, 2016)
1-92624267-T-C		not specified	Uncertain significance (Sep 13, 2023)
1-92624283-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-92624305-C-G		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVI5	protein_coding	protein_coding	ENST00000370331	18	283709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-11	0.998	125515	1	232	125748	0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.780	370	415	0.892	0.0000207	5359
Missense in Polyphen		65	100.84	0.64459		1282
Synonymous	0.598	134	143	0.936	0.00000748	1446
Loss of Function	2.86	25	45.9	0.545	0.00000229	562

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00919	0.00897
East Asian	0.000382	0.000381
Finnish	0.000673	0.000647
European (Non-Finnish)	0.000616	0.000598
Middle Eastern	0.000382	0.000381
South Asian	0.000664	0.000621
Other	0.000841	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a regulator of cell cycle progression by stabilizing the FBXO5 protein and promoting cyclin-A accumulation during interphase. May play a role in cytokinesis. {ECO:0000269|PubMed:16439210}.
• Disease: DISEASE: Note=A chromosomal aberration involving EVI5 is found is a patient with stage 4S neuroblastoma. Translocation t(1;10)(p22;q21) that forms a EVI5-TRNG10 fusion protein. TRNG10 is a probable structural transcript which is normally not translated. {ECO:0000269|PubMed:9618176}.
• Pathway: Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.975
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.13

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.694
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evi5
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: intracellular protein transport;cell cycle;multicellular organism development;cell population proliferation;retrograde transport, endosome to Golgi;positive regulation of GTPase activity;cell division;activation of GTPase activity;regulation of cilium assembly
• Cellular component: nucleus;Golgi apparatus;microtubule organizing center;spindle;cytosol;intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding