EVX2

even-skipped homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 2:176077472-176083962

Links

ENSG00000174279 ∙ NCBI:344191 ∙ OMIM:142991 ∙ HGNC:3507 ∙ Uniprot:Q03828 ∙ 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 EVX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVX2 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				3	1	4
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region		1				1
non coding						0
Total	0	0	34	5	1

Variants in EVX2

This is a list of pathogenic ClinVar variants found in the EVX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-176080128-G-C		EVX2-related disorder	Likely benign (Feb 15, 2022)
2-176080130-C-T		not specified	Uncertain significance (May 31, 2023)
2-176080163-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-176080183-G-C		not specified	Uncertain significance (Mar 07, 2023)
2-176080199-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-176080223-A-G		not specified	Uncertain significance (Jan 03, 2022)
2-176080231-T-C		not specified	Uncertain significance (Oct 29, 2021)
2-176080234-G-A		not specified	Uncertain significance (May 09, 2023)
2-176080273-C-T		not specified	Uncertain significance (Dec 07, 2023)
2-176080315-G-A		not specified	Uncertain significance (May 24, 2023)
2-176080330-G-A		not specified	Uncertain significance (May 14, 2024)
2-176080330-G-T		not specified	Uncertain significance (Sep 16, 2021)
2-176080334-C-T		not specified	Uncertain significance (Apr 06, 2023)
2-176080374-C-G			Likely benign (Jul 01, 2022)
2-176080381-G-A		not specified	Uncertain significance (Aug 30, 2021)
2-176080397-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-176080402-G-A		not specified	Uncertain significance (Sep 14, 2023)
2-176080424-A-G		not specified	Uncertain significance (Mar 25, 2024)
2-176080429-G-C		not specified	Uncertain significance (Sep 13, 2023)
2-176080446-T-G		EVX2-related disorder	Likely benign (Dec 13, 2021)
2-176080455-T-A		EVX2-related disorder	Likely benign (Jan 31, 2023)
2-176080455-TGCCGCGGCAGAGGCCGCGCTGTTGAGCCCCGCGGCG-T		EVX2-related disorder	Likely benign (Jan 08, 2021)
2-176080471-G-C		not specified	Uncertain significance (Oct 05, 2023)
2-176080575-G-C			Benign (Jul 04, 2018)
2-176080652-C-T		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVX2	protein_coding	protein_coding	ENST00000308618	3	6442

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.400	0.592	121578	0	2	121580	0.00000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.151	208	214	0.971	0.0000102	2936
Missense in Polyphen		38	57.001	0.66665		832
Synonymous	-0.513	103	96.6	1.07	0.00000502	1057
Loss of Function	2.22	2	9.32	0.215	4.00e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000973	0.00000906
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.131

Haploinsufficiency Scores

• pHI: 0.345
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evx2
• Phenotype: growth/size/body region phenotype; limbs/digits/tail phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype

Zebrafish Information Network

• Gene name: evx2
• Affected structure: spinal cord
• Phenotype tag: abnormal
• Phenotype quality: has extra parts of type

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process;limb morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding