CHDH choline dehydrogenase [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHDHprovided by HGNC
Official Full Name: choline dehydrogenaseprovided by HGNC
Primary source: HGNC:HGNC:24288
See related: Ensembl:ENSG00000016391 AllianceGenome:HGNC:24288
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
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]
Expression: Broad expression in kidney (RPKM 17.5), liver (RPKM 4.8) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (53812335..53846419, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (53845582..53879657, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (53846362..53880446, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

There is no correlation between single CHDH rs893363 and CHDH rs2289205 polymorphisms and the incidence of intrauterine fetal death.
Title: Polymorphic variants of genes involved in choline pathway and the risk of intrauterine fetal death.
CHDH gene is located at chromosome 3p21.1, a risk region implicated in previous brains of bipolar disorder genome-wide association studies
Title: Identification of a Bipolar Disorder Vulnerable Gene CHDH at 3p21.1.
In genotypic combination analysis considering PEMT -744GG/CHDH +432GG/BHMT +742GG as the reference combination, PEMT -744GC/CHDH +432GG/BHMT +742GG genotypic combination was significantly higher in mothers of a down syndrome child compared with that in control mothers with an odds ratio of 2.061 (95% CI: 1.10-3.86, P=0.0342).
Title: Choline metabolic pathway gene polymorphisms and risk for Down syndrome: An association study in a population with folate-homocysteine metabolic impairment.
CHDH is not a substrate of PARK2 but interacts with SQSTM1 independently of PARK2 to recruit SQSTM1 into depolarized mitochondria
Title: Choline dehydrogenase interacts with SQSTM1/p62 to recruit LC3 and stimulate mitophagy.
the PEMT -774G>C and CHDH +432G>T polymorphisms were associated with sperm concentration. This finding suggests a possible influence of these genes on sperm quality
Title: Phosphatidylethanolamine N-methyltransferase and choline dehydrogenase gene polymorphisms are associated with human sperm concentration.
The rs12676 single nucleotide polymorphism is associated with altered sperm motility patterns and dysmorphic mitochondrial structure in sperm.
Title: Choline dehydrogenase polymorphism rs12676 is a functional variation and is associated with changes in human sperm cell function.
CHDH and PLD2 as novel candidate genes, the nucleotide variants of which could be associated with the risk of tooth agenesis.
Title: Polymorphisms in CHDH gene and the risk of tooth agenesis.
CHDH A119C and MTHFR C677T play an important role in modulating the homocysteine levels in Indian population.
Title: Single nucleotide polymorphisms in homocysteine metabolism pathway genes: association of CHDH A119C and MTHFR C677T with hyperhomocysteinemia.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts.
single nucleotide polymorphisms of choline-metabolizing genes, PEMT -774G>C (rs12325817) and CHDH +432G>T (rs12676), were found be related to breast cancer risk
Title: Choline metabolism and risk of breast cancer in a population-based study.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102217 (e-PCR)
- UniSTS:96551

A009Z06 (e-PCR)
- UniSTS:25643

G33005 (e-PCR)
- UniSTS:117582

SHGC-67307 (e-PCR)
- UniSTS:89991

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables choline dehydrogenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables choline dehydrogenase activity	TAS Traceable Author Statement more info
enables flavin adenine dinucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in choline catabolic process	TAS Traceable Author Statement more info
involved_in glycine betaine biosynthetic process from choline	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in mitochondrial inner membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial inner membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: choline dehydrogenase, mitochondrial

Names: CDH; CHD

NP_060867.2

EC 1.1.99.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_028042.1 RefSeqGene

Range

5001..35097

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_018397.5 → NP_060867.2 choline dehydrogenase, mitochondrial

See identical proteins and their annotated locations for NP_060867.2

Status: REVIEWED

Source sequence(s)

AC012467, AJ272267, BC034502, BE856786, CN285856

Consensus CDS

CCDS2873.1

UniProtKB/Swiss-Prot

Q8NE62, Q9NY17

Related

ENSP00000319851.5, ENST00000315251.11

Conserved Domains (3) summary

PRK02106
Location:40 → 594

PRK02106; choline dehydrogenase; Validated

pfam05199
Location:430 → 567

GMC_oxred_C; GMC oxidoreductase

cl21454
Location:116 → 339

NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins