PBX3

PBX homeobox 3, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 9:125747344-125967377

Links

ENSG00000167081 ∙ NCBI:5090 ∙ OMIM:176312 ∙ HGNC:8634 ∙ Uniprot:P40426 ∙ 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 PBX3 gene.

• Inborn genetic diseases (13 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBX3 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	13	0	0

Variants in PBX3

This is a list of pathogenic ClinVar variants found in the PBX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-125747475-C-G		not specified	Uncertain significance (Feb 12, 2024)
9-125747619-A-G		not specified	Uncertain significance (Jun 05, 2023)
9-125747625-G-C		not specified	Uncertain significance (Sep 29, 2023)
9-125748570-A-G		not specified	Uncertain significance (Apr 19, 2023)
9-125748585-C-G		not specified	Uncertain significance (Oct 26, 2022)
9-125748585-C-T		not specified	Uncertain significance (Feb 23, 2023)
9-125748621-CA-C		X-linked cone-rod dystrophy	Likely pathogenic (Jan 03, 2023)
9-125915800-C-T		not specified	Uncertain significance (Nov 09, 2022)
9-125915817-G-A		not specified	Uncertain significance (Jul 05, 2023)
9-125915824-C-T		not specified	Uncertain significance (Sep 20, 2023)
9-125929710-C-T		not specified	Uncertain significance (Oct 29, 2021)
9-125935561-A-C		X-linked cone-rod dystrophy	Uncertain significance (Jan 03, 2023)
9-125960784-C-CT		X-linked cone-rod dystrophy	Likely pathogenic (Jan 03, 2023)
9-125960786-G-GTA		X-linked cone-rod dystrophy	Likely pathogenic (Jan 03, 2023)
9-125962156-A-G		not specified	Uncertain significance (Oct 06, 2022)
9-125962180-A-C		not specified	Uncertain significance (Jan 22, 2024)
9-125962194-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-125963005-C-A			Likely benign (May 24, 2018)
9-125963025-G-A		not specified	Uncertain significance (Jun 11, 2021)
9-125963028-A-G		not specified	Uncertain significance (Apr 20, 2023)
9-125965904-A-G		not specified	Uncertain significance (Jun 21, 2023)
9-125965907-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBX3	protein_coding	protein_coding	ENST00000373489	9	220033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.363	0.637	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	147	242	0.608	0.0000123	2846
Missense in Polyphen		22	85.444	0.25748		1036
Synonymous	0.578	85	92.1	0.923	0.00000516	818
Loss of Function	3.37	5	22.1	0.226	0.00000119	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000108	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator that binds the sequence 5'- ATCAATCAA-3'.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Mesodermal Commitment Pathway;miR-509-3p alteration of YAP1-ECM axis (Consensus)

Recessive Scores

• pRec: 0.0726

Intolerance Scores

• loftool: 0.193
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.673
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbx3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; digestive/alimentary phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: regulation of respiratory gaseous exchange by neurological system process;anterior compartment pattern formation;posterior compartment specification;respiratory gaseous exchange;adult locomotory behavior;dorsal spinal cord development;positive regulation of transcription by RNA polymerase II;neuron development
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific