EVI2A

ecotropic viral integration site 2A

Basic information

Region (hg38): 17:31316409-31321749

Previous symbols: [ "EVI2" ]

Links

ENSG00000126860 ∙ NCBI:2123 ∙ OMIM:158380 ∙ HGNC:3499 ∙ Uniprot:P22794 ∙ 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 EVI2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVI2A 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	1	2
missense			12	3	2	17
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	12	5	4

Variants in EVI2A

This is a list of pathogenic ClinVar variants found in the EVI2A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-31318325-A-G		not specified	Uncertain significance (Jun 23, 2023)
17-31318338-C-T		not specified	Uncertain significance (Sep 22, 2023)
17-31318380-T-C		not specified	Uncertain significance (Dec 28, 2022)
17-31318388-A-C		not specified	Uncertain significance (Dec 17, 2021)
17-31318418-G-A		not specified	Uncertain significance (Sep 07, 2022)
17-31318443-C-T		not specified	Uncertain significance (Oct 03, 2022)
17-31318455-C-T			Likely benign (Jun 01, 2024)
17-31318473-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-31318487-T-C		See cases • EVI2A-related disorder	Benign/Likely benign (Jun 01, 2024)
17-31318491-G-A		not specified	Uncertain significance (Oct 14, 2021)
17-31318511-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-31318553-A-G		not specified	Uncertain significance (May 03, 2023)
17-31318565-G-T		not specified • NF1-related disorder	Conflicting classifications of pathogenicity (Apr 12, 2022)
17-31318616-A-G		not specified	Uncertain significance (May 11, 2022)
17-31318616-ATGT-A		Neurofibromatosis, type 1	Likely benign (May 28, 2019)
17-31318632-C-T		not specified	Uncertain significance (May 06, 2024)
17-31318653-A-C		not specified	Uncertain significance (Jun 05, 2024)
17-31318685-A-G		Cardiovascular phenotype;Hereditary cancer-predisposing syndrome	Benign (Aug 04, 2022)
17-31318714-G-T		EVI2A-related disorder	Likely benign (Jul 01, 2023)
17-31318775-G-C		not specified	Uncertain significance (Feb 26, 2024)
17-31318858-G-A		EVI2A-related disorder	Benign (Jun 06, 2019)
17-31318913-C-T		not specified	Likely benign (Jun 24, 2022)
17-31318976-T-C			Likely benign (Dec 01, 2023)
17-31319014-G-A		not specified • EVI2A-related disorder	Benign (Oct 17, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVI2A	protein_coding	protein_coding	ENST00000247270	2	4325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00204	0.758	125700	0	19	125719	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0942	140	137	1.02	0.00000658	1698
Missense in Polyphen		34	30.781	1.1046		382
Synonymous	-0.903	57	49.0	1.16	0.00000258	512
Loss of Function	0.923	5	7.78	0.643	4.01e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000428	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May complex with itself or/and other proteins within the membrane, to function as part of a cell-surface receptor.

Recessive Scores

• pRec: 0.0802

Intolerance Scores

• loftool: 0.362
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.664
• hipred: N
• hipred_score: 0.112
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evi2a

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: transmembrane signaling receptor activity