PBX2

PBX homeobox 2, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 6:32184732-32190202

Links

ENSG00000204304 ∙ NCBI:5089 ∙ OMIM:176311 ∙ HGNC:8633 ∙ Uniprot:P40425 ∙ 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 PBX2 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBX2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in PBX2

This is a list of pathogenic ClinVar variants found in the PBX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32186607-C-T		not specified	Uncertain significance (Dec 08, 2023)
6-32186639-C-T		not specified	Uncertain significance (Oct 26, 2022)
6-32186862-A-G		not specified	Uncertain significance (Jun 21, 2021)
6-32186893-C-T		not specified	Uncertain significance (Apr 08, 2022)
6-32187284-C-A		not specified	Uncertain significance (Oct 03, 2022)
6-32187332-C-T		not specified	Uncertain significance (Aug 04, 2023)
6-32187721-G-A		not specified	Uncertain significance (Jun 23, 2023)
6-32188361-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-32188366-G-A		not specified	Uncertain significance (Jun 29, 2022)
6-32188382-C-G		not specified	Uncertain significance (Dec 08, 2023)
6-32189716-C-T		not specified	Uncertain significance (Jun 29, 2022)
6-32189721-G-T		not specified	Uncertain significance (Sep 22, 2022)
6-32189738-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-32189795-T-C		not specified	Likely benign (Aug 26, 2022)
6-32189827-T-C		not specified	Uncertain significance (Feb 24, 2022)
6-32189876-C-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBX2	protein_coding	protein_coding	ENST00000375050	9	5452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00468	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	170	252	0.674	0.0000142	2761
Missense in Polyphen		34	70.397	0.48298		872
Synonymous	2.51	67	98.8	0.678	0.00000569	862
Loss of Function	3.97	1	20.3	0.0493	0.00000107	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000202	0.0000176
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator that binds the sequence 5'- ATCAATCAA-3'. Activates transcription of PF4 in complex with MEIS1. {ECO:0000269|PubMed:12609849}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.159
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.662
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbx2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; normal 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); respiratory system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: proximal/distal pattern formation;embryonic limb morphogenesis;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;protein binding;transcription factor binding