CHPF2

chondroitin polymerizing factor 2, the group of Beta 3-glycosyltransferases|MicroRNA protein coding host genes|Beta 4-glycosyltransferases

Basic information

Region (hg38): 7:151232483-151240979

Links

ENSG00000033100 ∙ NCBI:54480 ∙ OMIM:608037 ∙ HGNC:29270 ∙ Uniprot:Q9P2E5 ∙ 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 CHPF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHPF2 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			58	1	2	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	65	4	2

Variants in CHPF2

This is a list of pathogenic ClinVar variants found in the CHPF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-151234016-G-A		not specified	Uncertain significance (Oct 12, 2021)
7-151234046-C-A		not specified	Uncertain significance (Apr 09, 2024)
7-151234141-G-C		not specified	Uncertain significance (Aug 21, 2023)
7-151234148-T-C		not specified	Uncertain significance (Jan 23, 2023)
7-151234186-G-A		not specified	Likely benign (May 03, 2023)
7-151234189-C-T		not specified	Uncertain significance (Dec 16, 2023)
7-151234251-C-A		not specified	Uncertain significance (May 07, 2024)
7-151234257-C-T			Likely benign (Mar 01, 2022)
7-151235079-C-T		not specified	Uncertain significance (May 03, 2023)
7-151235094-G-A		not specified	Uncertain significance (Mar 30, 2024)
7-151235124-T-C		not specified	Uncertain significance (Aug 02, 2022)
7-151235136-G-A		not specified	Uncertain significance (Aug 28, 2023)
7-151235197-G-T		not specified	Uncertain significance (Nov 14, 2023)
7-151235295-T-G		not specified	Uncertain significance (Aug 02, 2021)
7-151235296-T-C		not specified	Uncertain significance (Aug 02, 2021)
7-151235305-A-G		not specified	Uncertain significance (Dec 28, 2023)
7-151235315-G-T		not specified	Uncertain significance (Nov 12, 2021)
7-151235353-C-T		not specified	Uncertain significance (Oct 12, 2022)
7-151235425-T-A		not specified	Uncertain significance (Aug 15, 2023)
7-151235425-T-C		not specified	Uncertain significance (Oct 06, 2021)
7-151235430-G-A		not specified	Uncertain significance (Feb 21, 2024)
7-151235436-G-A		not specified	Uncertain significance (Dec 19, 2022)
7-151235445-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-151235446-G-A		not specified	Uncertain significance (Jul 06, 2021)
7-151235452-G-C		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHPF2	protein_coding	protein_coding	ENST00000035307	4	6334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-17	0.0279	125449	2	296	125747	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.516	518	486	1.07	0.0000337	4848
Missense in Polyphen		148	142.71	1.0371		1423
Synonymous	0.0855	200	202	0.992	0.0000118	1766
Loss of Function	0.656	28	32.0	0.875	0.00000248	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00172	0.00170
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00287	0.00283
Finnish	0.000416	0.000416
European (Non-Finnish)	0.00108	0.00106
Middle Eastern	0.00287	0.00283
South Asian	0.00221	0.00213
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers glucuronic acid (GlcUA) from UDP-GlcUA to N- acetylgalactosamine residues on the non-reducing end of the elongating chondroitin polymer. Has no N- acetylgalactosaminyltransferase activity. {ECO:0000269|PubMed:12145278, ECO:0000269|PubMed:18316376}.
• Pathway: Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Chondroitin sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Proteoglycan biosynthesis;chondroitin sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism;chondroitin and dermatan biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.962
• rvis_EVS: 0.17
• rvis_percentile_EVS: 64.99

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.396
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chpf2

Gene ontology

• Biological process: chondroitin sulfate biosynthetic process
• Cellular component: Golgi membrane;membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: acetylgalactosaminyltransferase activity;N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity