CHDH
Basic information
Region (hg38): 3:53812335-53846419
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (96 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHDH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018397.5. 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 89 | 96 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 89 | 8 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CHDH | protein_coding | protein_coding | ENST00000315251 | 7 | 34056 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000168 | 0.967 | 125673 | 0 | 75 | 125748 | 0.000298 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.02 | 321 | 377 | 0.852 | 0.0000254 | 3781 |
Missense in Polyphen | 136 | 171.52 | 0.79291 | 1620 | ||
Synonymous | 0.352 | 161 | 167 | 0.965 | 0.0000123 | 1224 |
Loss of Function | 1.99 | 13 | 23.4 | 0.555 | 0.00000115 | 244 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000813 | 0.000812 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.0000555 | 0.0000544 |
Finnish | 0.0000965 | 0.0000924 |
European (Non-Finnish) | 0.000367 | 0.000343 |
Middle Eastern | 0.0000555 | 0.0000544 |
South Asian | 0.000302 | 0.000294 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Pathway
- Glycine, serine and threonine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Betaine Metabolism;Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;sarcosine oncometabolite pathway ;Cystathionine Beta-Synthase Deficiency;Methionine De Novo and Salvage Pathway;One carbon metabolism and related pathways;choline degradation;Metabolism of amino acids and derivatives;Metabolism;Choline catabolism;superpathway of choline degradation to L-serine;Glycine, serine, alanine and threonine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- loftool
- 0.581
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.51
Haploinsufficiency Scores
- pHI
- 0.152
- hipred
- N
- hipred_score
- 0.343
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chdh
- Phenotype
- cellular phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- glycine betaine biosynthetic process from choline;choline catabolic process;oxidation-reduction process
- Cellular component
- mitochondrial inner membrane
- Molecular function
- protein binding;choline dehydrogenase activity;flavin adenine dinucleotide binding