CHDH

protein-coding

choline dehydrogenase

Gene summary

The protein encoded by this gene is a choline dehydrogenase that localizes to the mitochondrion. Variations in this gene can affect susceptibility to choline deficiency. A few transcript variants have been found for this gene, but the full-length nature of only one has been characterized to date. [provided by RefSeq, Dec 2010]

MANE transcript

NM_018397.5

Inheritance

—

ClinVar variants

U:102B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr3:53,812,335-53,846,419

External References & Databases

Ensembl (ENSG00000016391)

Transcript & Mutation Effects

hg38 • Region Span ~34.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHDH variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018397.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	3 clinvar	4
missense			100 clinvar	7 clinvar		107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	102	8	3	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018397.5	RefSeq	NP_060867.2	7	MANE Select
ENST00000315251.11	Ensembl	ENSP00000319851.5	7	MANE Select
ENST00000467802.1	Ensembl	ENSP00000419863.1	1	Standard
ENST00000481668.5	Ensembl	ENSP00000418273.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycine, serine and threonine metabolism - Homo sapiens (human)
S-Adenosylhomocysteine (SAH) Hydrolase Deficiency
Methionine Metabolism
Methionine Adenosyltransferase Deficiency
Glycine N-methyltransferase Deficiency

Biological Process

glycine betaine biosynthetic process from choline
choline catabolic process
oxidation-reduction process

Molecular Function

protein binding
choline dehydrogenase activity
flavin adenine dinucleotide binding

Cellular Component

mitochondrial inner membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315251
Coding exons: 7
Length: 34056
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 75
Defined: 125748
p: 0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.02	321	377	0.852	0.0000254	3781
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00050	0.00049	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000055	0.000054	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00037	0.00034	rare
South Asian	0.00030	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.177

Intolerance Scores

LoFtool: 0.581
RVIS EVS: -0.49
RVIS percentile EVS: 22.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.945

Gene Damage Prediction

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