CHPF

chondroitin polymerizing factor, the group of Beta 4-glycosyltransferases|Beta 3-glycosyltransferases

Basic information

Region (hg38): 2:219538954-219543809

Links

ENSG00000123989 ∙ NCBI:79586 ∙ OMIM:610405 ∙ HGNC:24291 ∙ Uniprot:Q8IZ52 ∙ 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 CHPF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHPF 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			50	2	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	2	2

Variants in CHPF

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

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

Position	Type	Phenotype	Significance	ClinVar
2-219539397-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-219539432-G-T		not specified	Uncertain significance (Oct 14, 2023)
2-219539477-T-G		not specified	Uncertain significance (Jun 22, 2024)
2-219539490-T-C		not specified	Uncertain significance (Jun 16, 2024)
2-219539499-C-T		not specified	Uncertain significance (May 18, 2023)
2-219539517-G-A		not specified	Uncertain significance (Apr 04, 2024)
2-219539522-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-219539546-G-A		not specified	Uncertain significance (Jan 02, 2024)
2-219539565-T-C		not specified	Likely benign (Dec 03, 2021)
2-219539577-G-A		not specified	Uncertain significance (Sep 22, 2023)
2-219539580-A-T		not specified	Uncertain significance (Aug 04, 2023)
2-219539612-T-A		not specified	Uncertain significance (Oct 06, 2021)
2-219539613-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-219539614-C-T			Benign (Dec 31, 2019)
2-219539616-C-G		not specified	Uncertain significance (Sep 29, 2023)
2-219539619-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-219539619-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-219539625-C-G		not specified	Uncertain significance (May 23, 2023)
2-219539685-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-219539765-G-C		not specified	Uncertain significance (Apr 01, 2024)
2-219539785-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-219539800-C-G		not specified	Uncertain significance (Jan 04, 2022)
2-219539831-C-T		not specified	Uncertain significance (Jul 11, 2023)
2-219539868-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-219539969-C-T		not specified	Uncertain significance (Feb 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHPF	protein_coding	protein_coding	ENST00000243776	4	4841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.151	0.849	125678	0	68	125746	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	419	483	0.868	0.0000317	4803
Missense in Polyphen		87	113.4	0.7672		1155
Synonymous	1.18	188	210	0.896	0.0000125	1762
Loss of Function	3.33	6	23.4	0.257	0.00000143	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000364	0.000360
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000508	0.000484
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000688	0.0000653
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has both beta-1,3-glucuronic acid and beta-1,4-N- acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Isoform 2 may facilitate PRKN transport into the mitochondria. In collaboration with PRKN, isoform 2 may enhance cell viability and protect cells from oxidative stress. {ECO:0000269|PubMed:12761225}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;chondroitin sulfate biosynthesis (late stages);Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism;chondroitin and dermatan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.196

Intolerance Scores

• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.89

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.597
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.323

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chpf
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; normal phenotype

Gene ontology

• Biological process: chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;mitochondrial matrix;cytosol;integral component of membrane;Golgi cisterna membrane
• Molecular function: metal ion binding;glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity;N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity