EVX1

even-skipped homeobox 1, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 7:27242699-27250493

Links

ENSG00000106038 ∙ NCBI:2128 ∙ OMIM:142996 ∙ HGNC:3506 ∙ Uniprot:P49640 ∙ 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 EVX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVX1 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
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	1

Variants in EVX1

This is a list of pathogenic ClinVar variants found in the EVX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-27243051-G-A		not specified	Uncertain significance (Dec 15, 2021)
7-27243051-G-T		not specified	Uncertain significance (Jul 11, 2023)
7-27243079-G-T		not specified	Uncertain significance (Jun 11, 2024)
7-27243121-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-27243217-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-27243218-G-A		not specified	Uncertain significance (Mar 07, 2023)
7-27243232-G-A		not specified	Uncertain significance (Nov 27, 2023)
7-27243359-C-A		not specified	Uncertain significance (Dec 07, 2022)
7-27243430-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-27243439-G-A		not specified	Uncertain significance (Jan 26, 2022)
7-27245111-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-27245231-G-T		not specified	Uncertain significance (Nov 17, 2023)
7-27245957-C-A		not specified	Uncertain significance (Jan 26, 2022)
7-27245976-A-G		not specified	Uncertain significance (Dec 11, 2023)
7-27246010-C-A		not specified	Uncertain significance (Oct 03, 2023)
7-27246025-C-G		not specified	Uncertain significance (Apr 06, 2022)
7-27246025-C-T		not specified	Uncertain significance (Dec 07, 2023)
7-27246039-C-T		not specified	Uncertain significance (May 27, 2022)
7-27246071-A-C			Benign (Jan 30, 2018)
7-27246094-C-T		not specified	Uncertain significance (Jul 07, 2022)
7-27246105-G-T		not specified	Uncertain significance (Sep 14, 2022)
7-27246114-C-A		not specified	Uncertain significance (Feb 06, 2023)
7-27246115-G-A		not specified	Uncertain significance (Mar 17, 2023)
7-27246133-G-T		not specified	Uncertain significance (Jul 06, 2021)
7-27246157-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVX1	protein_coding	protein_coding	ENST00000496902	3	7949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.98e-7	0.285	125715	0	14	125729	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.805	256	222	1.15	0.0000102	2511
Missense in Polyphen		77	80.053	0.96186		927
Synonymous	-2.37	136	105	1.29	0.00000511	899
Loss of Function	0.305	10	11.1	0.901	4.82e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000593	0.0000593
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000746	0.0000703
Middle Eastern	0.000110	0.000109
South Asian	0.0000661	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the specification of neuronal cell types.

Recessive Scores

• pRec: 0.127

Haploinsufficiency Scores

• pHI: 0.694
• hipred: Y
• hipred_score: 0.603
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Evx1
• Phenotype: embryo 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: evx1
• Affected structure: lepidotrichium
• Phenotype tag: abnormal
• Phenotype quality: undivided

Gene ontology

• Biological process: embryo development ending in birth or egg hatching;regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding