EVI2B

ecotropic viral integration site 2B, the group of CD molecules

Basic information

Region (hg38): 17:31303769-31314105

Links

ENSG00000185862 ∙ NCBI:2124 ∙ OMIM:158381 ∙ HGNC:3500 ∙ Uniprot:P34910 ∙ 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 EVI2B gene.

• Inborn genetic diseases (24 variants)
• not provided (8 variants)
• not specified (1 variants)
• Neurofibromatosis, type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVI2B 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					2	2
missense			20	7	1	28
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	7	3

Variants in EVI2B

This is a list of pathogenic ClinVar variants found in the EVI2B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-31304305-A-T		not specified	Uncertain significance (Jan 31, 2022)
17-31304387-A-G		not specified	Uncertain significance (Jan 05, 2022)
17-31304396-A-G		not specified	Uncertain significance (Jul 14, 2021)
17-31304432-T-C		not specified	Uncertain significance (Apr 18, 2023)
17-31304483-G-T		not specified	Uncertain significance (Feb 02, 2024)
17-31304517-G-C		not specified	Uncertain significance (Jun 10, 2022)
17-31304532-T-C		not specified	Uncertain significance (Apr 11, 2023)
17-31304591-G-C		Neurofibromatosis, type 1	Benign/Likely benign (Mar 15, 2022)
17-31304601-C-G		not specified	Uncertain significance (Mar 28, 2022)
17-31304615-G-T		not specified	Uncertain significance (Jan 18, 2022)
17-31304654-T-C		not specified	Uncertain significance (Dec 18, 2023)
17-31304672-A-G		not specified	Uncertain significance (Aug 02, 2023)
17-31304679-C-G		not specified	Uncertain significance (Aug 17, 2022)
17-31304757-C-G			Benign (Feb 01, 2024)
17-31304814-G-A		not specified	Uncertain significance (Oct 14, 2023)
17-31304847-C-T		not specified	Uncertain significance (Apr 06, 2023)
17-31304852-C-A			Benign/Likely benign (Jan 03, 2019)
17-31304902-T-A		not specified	Uncertain significance (May 27, 2022)
17-31304931-A-T			Likely benign (Mar 01, 2023)
17-31304952-T-C		not specified	Uncertain significance (May 08, 2023)
17-31304967-T-C		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
17-31305016-GT-G		not specified	Uncertain significance (May 04, 2022)
17-31305152-A-G		not specified	Uncertain significance (Oct 12, 2022)
17-31305159-A-T		not specified	Uncertain significance (Dec 15, 2023)
17-31305164-T-G		not specified	Uncertain significance (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVI2B	protein_coding	protein_coding	ENST00000330927	1	10347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0633	0.923	125705	0	40	125745	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.167	215	222	0.969	0.0000104	2906
Missense in Polyphen		45	57.37	0.78439		671
Synonymous	-0.368	85	80.8	1.05	0.00000373	933
Loss of Function	2.14	4	12.0	0.333	5.23e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000532	0.000532
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for granulocyte differentiation and functionality of hematopoietic progenitor cells through the control of cell cycle progression and survival of hematopoietic progenitor cells. {ECO:0000269|PubMed:28186500}.

Recessive Scores

• pRec: 0.0864

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.0854
• hipred: N
• hipred_score: 0.145
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00101

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evi2b

Gene ontology

• Biological process: positive regulation of granulocyte differentiation;negative regulation of apoptotic process;positive regulation of neutrophil differentiation;myeloid cell development;negative regulation of cell cycle arrest;regulation of stem cell division
• Cellular component: integral component of plasma membrane