PAXBP1

PAX3 and PAX7 binding protein 1

Basic information

Region (hg38): 21:32733899-32771792

Previous symbols: [ "C21orf66", "GCFC1" ]

Links

ENSG00000159086 ∙ NCBI:94104 ∙ OMIM:617621 ∙ HGNC:13579 ∙ Uniprot:Q9Y5B6 ∙ 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 PAXBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAXBP1 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					1	1
missense			52	3		55
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	52	3	1

Variants in PAXBP1

This is a list of pathogenic ClinVar variants found in the PAXBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32734996-C-T		not specified	Uncertain significance (May 06, 2022)
21-32737332-C-G		not specified	Uncertain significance (Nov 09, 2023)
21-32738186-T-C		not specified	Uncertain significance (Sep 16, 2021)
21-32743263-A-C		not specified	Uncertain significance (Aug 04, 2023)
21-32743320-T-TA			Likely benign (Sep 01, 2022)
21-32743731-C-G		not specified	Uncertain significance (Feb 28, 2024)
21-32744811-G-T		not specified	Uncertain significance (Dec 23, 2024)
21-32744819-T-G			Benign (Sep 19, 2018)
21-32745640-T-G		not specified	Uncertain significance (Dec 12, 2024)
21-32745713-T-G		not specified	Uncertain significance (May 17, 2023)
21-32748542-T-C		not specified	Uncertain significance (May 26, 2023)
21-32748570-T-C		not specified	Uncertain significance (Dec 28, 2022)
21-32748639-T-C		not specified	Uncertain significance (Jun 27, 2023)
21-32748644-T-C		not specified	Uncertain significance (May 15, 2023)
21-32750997-T-C		not specified	Uncertain significance (Jan 30, 2024)
21-32751027-C-T		not specified	Uncertain significance (Dec 19, 2022)
21-32751028-G-A			Uncertain significance (Jul 16, 2020)
21-32751180-G-A		not specified	Uncertain significance (Mar 16, 2022)
21-32751186-A-G		not specified	Uncertain significance (Jul 20, 2021)
21-32755320-G-A		not specified	Uncertain significance (May 15, 2024)
21-32755321-T-C		not specified	Uncertain significance (Mar 30, 2024)
21-32755325-G-C		not specified	Uncertain significance (Dec 21, 2024)
21-32759144-C-T		not specified	Uncertain significance (Mar 30, 2024)
21-32759204-C-T		not specified	Uncertain significance (Aug 08, 2022)
21-32759897-G-A		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAXBP1	protein_coding	protein_coding	ENST00000331923	18	37960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000672	125735	0	8	125743	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	306	468	0.653	0.0000249	5986
Missense in Polyphen		51	134.49	0.37922		1614
Synonymous	1.03	147	164	0.897	0.00000816	1681
Loss of Function	6.28	5	55.4	0.0902	0.00000354	627

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000172	0.000165
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein linking the transcription factors PAX3 and PAX7 to the histone methylation machinery and involved in myogenesis. Associates with a histone methyltransferase complex that specifically mediates dimethylation and trimethylation of 'Lys-4' of histone H3. Mediates the recruitment of that complex to the transcription factors PAX3 and PAX7 on chromatin to regulate the expression of genes involved in muscle progenitor cells proliferation including ID3 and CDC20 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.73

Haploinsufficiency Scores

• pHI: 0.470
• hipred: Y
• hipred_score: 0.768
• ghis: 0.607

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Paxbp1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;muscle organ development;regulation of skeletal muscle satellite cell proliferation;positive regulation of histone methylation;positive regulation of transcription by RNA polymerase II;positive regulation of myoblast proliferation
• Cellular component: nucleus;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;transcription factor binding