PBXIP1

PBX homeobox interacting protein 1

Basic information

Region (hg38): 1:154944075-154956123

Links

ENSG00000163346 ∙ NCBI:57326 ∙ OMIM:618819 ∙ HGNC:21199 ∙ Uniprot:Q96AQ6 ∙ 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 PBXIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PBXIP1 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				3		3
missense			44	3		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	6	0

Variants in PBXIP1

This is a list of pathogenic ClinVar variants found in the PBXIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-154945031-C-T		not specified	Uncertain significance (May 31, 2023)
1-154945032-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-154945049-C-T		not specified	Uncertain significance (Jun 27, 2022)
1-154945116-A-G		not specified	Uncertain significance (Mar 20, 2023)
1-154945705-G-A		not specified	Uncertain significance (Aug 31, 2022)
1-154945716-C-T		not specified	Uncertain significance (May 23, 2023)
1-154945725-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-154945749-A-C		not specified	Uncertain significance (Dec 08, 2023)
1-154945758-G-A		not specified	Uncertain significance (May 24, 2024)
1-154945809-T-A		not specified	Uncertain significance (Sep 17, 2021)
1-154945827-G-A		not specified	Uncertain significance (May 28, 2024)
1-154945866-A-G		not specified	Uncertain significance (Dec 13, 2021)
1-154945893-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-154945897-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-154945926-C-T		not specified	Uncertain significance (May 20, 2024)
1-154945998-C-T		not specified	Likely benign (Feb 06, 2024)
1-154946186-T-G		not specified	Uncertain significance (Feb 12, 2024)
1-154946199-T-C		not specified	Uncertain significance (Jan 22, 2024)
1-154946220-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-154946279-G-T		not specified	Uncertain significance (Oct 12, 2022)
1-154946310-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-154946375-G-A			Likely benign (Oct 01, 2023)
1-154946410-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-154946412-C-A		not specified	Uncertain significance (Feb 24, 2022)
1-154946413-G-A		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PBXIP1	protein_coding	protein_coding	ENST00000368463	10	12048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.79e-11	0.906	125650	0	98	125748	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.793	363	408	0.890	0.0000232	4726
Missense in Polyphen		95	122.64	0.77463		1477
Synonymous	1.31	145	167	0.870	0.00000856	1486
Loss of Function	1.91	21	32.8	0.640	0.00000159	353

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00100
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.000363	0.000352
Middle Eastern	0.000979	0.000979
South Asian	0.000524	0.000523
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of pre-B-cell leukemia transcription factors (BPXs) function. Inhibits the binding of PBX1-HOX complex to DNA and blocks the transcriptional activity of E2A-PBX1. Tethers estrogen receptor-alpha (ESR1) to microtubules and allows them to influence estrogen receptors-alpha signaling. {ECO:0000269|PubMed:10825160, ECO:0000269|PubMed:12360403, ECO:0000269|PubMed:17043237}.

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• loftool: 0.936
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.28

Haploinsufficiency Scores

• pHI: 0.0791
• hipred: N
• hipred_score: 0.145
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pbxip1

Gene ontology

• Biological process: multicellular organism development;cell differentiation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytosol;microtubule
• Molecular function: transcription corepressor activity;protein binding