PBX4

PBX homeobox 4, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:19561706-19618693

Links

ENSG00000105717 ∙ NCBI:80714 ∙ OMIM:608127 ∙ HGNC:13403 ∙ Uniprot:Q9BYU1 ∙ 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 PBX4 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBX4 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in PBX4

This is a list of pathogenic ClinVar variants found in the PBX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19563529-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-19563588-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-19564961-G-T		not specified	Likely benign (Jul 12, 2023)
19-19564986-G-A		not specified	Uncertain significance (Sep 22, 2022)
19-19564996-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-19565001-G-A		not specified	Uncertain significance (Jun 05, 2023)
19-19569463-G-A		not specified	Uncertain significance (Dec 02, 2022)
19-19569483-T-C		not specified	Uncertain significance (Jun 22, 2021)
19-19569493-C-A		not specified	Uncertain significance (Jan 06, 2023)
19-19569511-G-T		not specified	Uncertain significance (Jan 19, 2024)
19-19569555-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-19569577-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-19569579-T-C		not specified	Uncertain significance (Mar 31, 2022)
19-19570130-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-19570182-C-T		not specified	Uncertain significance (Mar 07, 2023)
19-19570268-T-C		not specified	Uncertain significance (Nov 12, 2021)
19-19570293-G-A		not specified	Uncertain significance (Feb 24, 2023)
19-19570654-A-G		not specified	Uncertain significance (Aug 10, 2021)
19-19570744-T-C		not specified	Uncertain significance (Aug 12, 2021)
19-19570750-C-T		not specified	Uncertain significance (May 10, 2022)
19-19570816-T-C		not specified	Uncertain significance (May 03, 2023)
19-19570822-G-A		not specified	Uncertain significance (Oct 27, 2022)
19-19599328-G-C		not specified	Uncertain significance (Nov 30, 2021)
19-19618551-T-G		not specified	Uncertain significance (Mar 11, 2024)
19-19618589-G-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBX4	protein_coding	protein_coding	ENST00000251203	8	57204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000526	0.887	125522	0	226	125748	0.000899

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.668	194	222	0.874	0.0000135	2409
Missense in Polyphen		50	70.943	0.70479		919
Synonymous	0.649	86	94.0	0.915	0.00000634	756
Loss of Function	1.48	9	15.2	0.592	7.29e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00465	0.00465
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000379	0.000378
Middle Eastern	0.00	0.00
South Asian	0.00157	0.00157
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.389
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.167
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.577

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbx4

Zebrafish Information Network

• Gene name: pbx4
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of transcription, DNA-templated
• Cellular component: XY body;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding