LDHC

protein-coding

lactate dehydrogenase C

Gene summary

Lactate dehydrogenase C catalyzes the conversion of L-lactate and NAD to pyruvate and NADH in the final step of anaerobic glycolysis. LDHC is testis-specific and belongs to the lactate dehydrogenase family. Two transcript variants have been detected which differ in the 5' untranslated region. [provided by RefSeq, Jul 2008]

MANE transcript

NM_017448.5

Inheritance

—

ClinVar variants

U:41B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr11:18,412,318-18,452,063

External References & Databases

Ensembl (ENSG00000166796)

Transcript & Mutation Effects

hg38 • Region Span ~39.7 kb

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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 LDHC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017448.5. 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						0
missense			40 clinvar	1 clinvar	1 clinvar	42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	41	1	1	43

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017448.5	RefSeq	NP_059144.1	7	MANE Select
ENST00000541669.6	Ensembl	ENSP00000437783.1	7	MANE Select
NM_002301.5	RefSeq	NP_002292.1	7	Standard
ENST00000280704.8	Ensembl	ENSP00000280704.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyruvate metabolism - Homo sapiens (human)
Glycolysis / Gluconeogenesis - Homo sapiens (human)
Propanoate metabolism - Homo sapiens (human)
Cysteine and methionine metabolism - Homo sapiens (human)
Glucagon signaling pathway - Homo sapiens (human)

Biological Process

carbohydrate metabolic process
pyruvate metabolic process
ATP biosynthetic process
lactate biosynthetic process from pyruvate
lactate oxidation

Molecular Function

L-lactate dehydrogenase activity

Cellular Component

nucleus
cytosol
motile cilium
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000541669
Coding exons: 7
Length: 39752
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125746
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.169	171	177	0.964	0.00000880	2166
Missense (PolyPhen)		69	83.658	0.82478		1048
Synonymous	1.20	48	59.8	0.802	0.00000274	652
Loss of Function	0.673	11	13.7	0.804	5.75e-7	185

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00054	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in sperm motility.;

Recessive Scores

pRec: 0.536

Intolerance Scores

LoFtool: 0.383
RVIS EVS: 0.42
RVIS percentile EVS: 76.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.846

Gene Damage Prediction

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