GeneBe

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.

  • not_specified (118 variants)
  • not_provided (5 variants)

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. These statistics are base on transcript: NM_000019015.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
 3
missense
115
clinvar
4
clinvar
1
clinvar
 120
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 115 7 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CHPF2protein_codingprotein_codingENST00000035307 46334
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.19e-170.027912544922961257470.00119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5165184861.070.00003374848
Missense in Polyphen148142.711.03711423
Synonymous0.08552002020.9920.00001181766
Loss of Function0.6562832.00.8750.00000248260

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001720.00170
Ashkenazi Jewish0.0001980.000198
East Asian0.002870.00283
Finnish0.0004160.000416
European (Non-Finnish)0.001080.00106
Middle Eastern0.002870.00283
South Asian0.002210.00213
Other0.001160.00114

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

pHI
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Chpf2
Phenotype

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