LDHC

lactate dehydrogenase C

Basic information

Region (hg38): 11:18412318-18452063

Links

ENSG00000166796 ∙ NCBI:3948 ∙ OMIM:150150 ∙ HGNC:6544 ∙ Uniprot:P07864 ∙ 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 LDHC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDHC 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						0
missense			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	1

Variants in LDHC

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

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

Position	Type	Phenotype	Significance	ClinVar
11-18412724-A-G		not specified	Uncertain significance (Mar 29, 2022)
11-18412754-A-C			Benign (Jul 06, 2018)
11-18412755-T-C		not specified	Uncertain significance (Nov 30, 2021)
11-18412777-G-C		not specified	Uncertain significance (Jun 21, 2023)
11-18415215-T-C		not specified	Uncertain significance (Nov 07, 2023)
11-18415226-A-G		not specified	Uncertain significance (Dec 23, 2022)
11-18429752-C-G		not specified	Uncertain significance (Feb 05, 2024)
11-18429840-A-G		not specified	Uncertain significance (Jun 23, 2023)
11-18429842-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-18434788-C-G		not specified	Uncertain significance (Mar 27, 2023)
11-18434796-A-G		not specified	Uncertain significance (Feb 07, 2023)
11-18434802-A-G		not specified	Uncertain significance (Dec 05, 2022)
11-18434826-C-T		not specified	Uncertain significance (Aug 16, 2021)
11-18434848-A-G		not specified	Uncertain significance (May 17, 2023)
11-18434902-G-A		not specified	Uncertain significance (Apr 05, 2023)
11-18438593-A-G		not specified	Uncertain significance (Nov 27, 2023)
11-18438594-C-T		not specified	Uncertain significance (Nov 17, 2023)
11-18446239-A-G		not specified	Uncertain significance (Apr 25, 2022)
11-18446286-A-G		not specified	Uncertain significance (Jul 30, 2023)
11-18450964-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-18451043-A-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDHC	protein_coding	protein_coding	ENST00000541669	7	39752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-7	0.426	125682	0	64	125746	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	171	177	0.964	0.00000880	2166
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000582	0.000576
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.0000544	0.0000544
South Asian	0.000541	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in sperm motility.
• Pathway: 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);Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;Glycolysis Gluconeogenesis;lactate fermentation (reoxidation of cytosolic NADH);The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Methionine Cysteine metabolism;Propanoate metabolism;Pyruvate metabolism (Consensus)

Recessive Scores

• pRec: 0.536

Intolerance Scores

• loftool: 0.383
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.0636
• hipred: N
• hipred_score: 0.213

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldhc
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;pyruvate metabolic process;ATP biosynthetic process;lactate biosynthetic process from pyruvate;lactate oxidation;flagellated sperm motility
• Cellular component: nucleus;cytosol;motile cilium;extracellular exosome
• Molecular function: L-lactate dehydrogenase activity