CHDH

choline dehydrogenase

Basic information

Region (hg38): 3:53812334-53846419

Links

ENSG00000016391 ∙ NCBI:55349 ∙ ∙ HGNC:24288 ∙ Uniprot:Q8NE62 ∙ 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 CHDH gene.

• Inborn genetic diseases (24 variants)
• not provided (5 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.

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	2	3
missense			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	21	4	2

Variants in CHDH

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

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

Position	Type	Phenotype	Significance	ClinVar
3-53817851-T-A		not specified	Uncertain significance (Oct 14, 2023)
3-53817890-C-T		not specified	Uncertain significance (Nov 14, 2023)
3-53817895-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-53817995-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-53818026-G-C			Likely benign (Aug 08, 2018)
3-53818046-C-T		not specified	Uncertain significance (Jul 06, 2022)
3-53818060-A-G		not specified	Uncertain significance (Nov 07, 2023)
3-53818071-C-G		not specified	Uncertain significance (Jun 10, 2022)
3-53818111-T-C		not specified	Uncertain significance (Jan 29, 2024)
3-53818174-C-T		not specified	Uncertain significance (Oct 13, 2021)
3-53818940-G-T		not specified	Uncertain significance (May 11, 2022)
3-53819558-C-T		not specified	Uncertain significance (Mar 14, 2024)
3-53819608-G-A		not specified	Uncertain significance (Oct 22, 2021)
3-53819670-C-G		not specified	Likely benign (Sep 20, 2023)
3-53820477-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-53820515-C-T		not specified	Likely benign (May 27, 2022)
3-53820516-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-53820551-C-T		not specified	Likely benign (Jul 14, 2021)
3-53820606-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-53821737-T-C		not specified	Uncertain significance (Oct 27, 2022)
3-53822498-C-G		not specified	Uncertain significance (Nov 22, 2021)
3-53822526-C-T		not specified	Uncertain significance (Jun 07, 2023)
3-53822628-C-T		not specified	Likely benign (Feb 16, 2023)
3-53822637-G-A		not specified	Uncertain significance (Apr 18, 2023)
3-53822641-G-A			Benign (Mar 02, 2018)

GnomAD

Source: gnomAD

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: dbNSFP

• 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