VENTX

VENT homeobox, the group of NKL subclass homeoboxes and pseudogenes

Basic information

Region (hg38): 10:133237855-133241928

Previous symbols: [ "VENTX2" ]

Links

ENSG00000151650 ∙ NCBI:27287 ∙ OMIM:607158 ∙ HGNC:13639 ∙ Uniprot:O95231 ∙ 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 VENTX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VENTX 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						0
missense			20	4		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	0

Variants in VENTX

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

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

Position	Type	Phenotype	Significance	ClinVar
10-133237939-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-133237952-A-C		not specified	Likely benign (Dec 28, 2022)
10-133238047-C-A		not specified	Uncertain significance (Nov 29, 2021)
10-133238066-C-G		not specified	Uncertain significance (Jul 31, 2023)
10-133238083-C-A		not specified	Uncertain significance (Aug 17, 2022)
10-133238120-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-133239703-G-T		not specified	Uncertain significance (Dec 15, 2022)
10-133239733-T-G		not specified	Uncertain significance (Mar 06, 2023)
10-133239744-C-T		not specified	Uncertain significance (Oct 13, 2023)
10-133239745-G-A		not specified	Uncertain significance (Jun 11, 2021)
10-133239787-C-T		not specified	Uncertain significance (Jul 13, 2021)
10-133239957-G-A		not specified	Uncertain significance (Jun 13, 2024)
10-133239969-A-G		not specified	Uncertain significance (Oct 03, 2022)
10-133239972-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-133239996-A-G		not specified	Uncertain significance (Dec 26, 2023)
10-133240002-C-A		not specified	Uncertain significance (Nov 17, 2022)
10-133240004-T-C		not specified	Uncertain significance (Sep 26, 2022)
10-133240008-C-T		not specified	Likely benign (Aug 12, 2021)
10-133240023-C-T		not specified	Likely benign (Feb 07, 2023)
10-133240050-C-G		not specified	Uncertain significance (Mar 06, 2023)
10-133240130-T-C		not specified	Uncertain significance (Nov 07, 2022)
10-133240193-G-A		not specified	Likely benign (Oct 12, 2021)
10-133240208-T-A		not specified	Uncertain significance (Dec 21, 2022)
10-133240230-G-A		not specified	Uncertain significance (Jun 12, 2023)
10-133240290-C-G		not specified	Uncertain significance (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VENTX	protein_coding	protein_coding	ENST00000325980	3	4526

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000275	0.190	125569	0	8	125577	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.669	180	156	1.15	0.00000931	1617
Missense in Polyphen		40	36.975	1.0818		382
Synonymous	-0.655	75	68.1	1.10	0.00000388	570
Loss of Function	-0.724	6	4.37	1.37	1.86e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000836	0.0000617
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000270	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in ventralization.

Recessive Scores

• pRec: 0.0818

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.372

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding