LDHD

lactate dehydrogenase D

Basic information

Region (hg38): 16:75111860-75116780

Links

ENSG00000166816 ∙ NCBI:197257 ∙ OMIM:607490 ∙ HGNC:19708 ∙ Uniprot:Q86WU2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
D-lactic aciduria	AR	Renal	The condition can manifest with gouty arthropathy, and medical (eg, with colchicine and allopurinol) and dietary management (eg, related to meat consumption) has been reported as beneficial	Biochemical; Musculoskeletal; Neurologic; Renal	30931947; 31638601

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LDHD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDHD 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		2	49		3	54
nonsense			1			1
start loss						0
frameshift		1	1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	3	51	1	6

Variants in LDHD

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

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

Position	Type	Phenotype	Significance	ClinVar
16-75112414-C-T		not specified	Uncertain significance (Jun 06, 2022)
16-75112417-A-G		Lactic aciduria due to D-lactic acid	Uncertain significance (May 31, 2020)
16-75112432-A-T		not specified	Uncertain significance (Jan 08, 2025)
16-75112433-C-T		not specified	Uncertain significance (Oct 07, 2024)
16-75112459-T-G		not specified	Uncertain significance (Sep 30, 2021)
16-75112475-C-T		not specified	Uncertain significance (Jun 01, 2023)
16-75112478-T-C		not specified	Uncertain significance (Sep 16, 2021)
16-75112492-G-A		Abnormal circulating lactate dehydrogenase concentration • Lactic aciduria due to D-lactic acid	Likely pathogenic (Oct 15, 2024)
16-75112498-G-A		not specified	Uncertain significance (Jan 21, 2025)
16-75112516-G-GC		Lactic aciduria due to D-lactic acid	Pathogenic (Nov 20, 2024)
16-75112520-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-75112520-G-C		not specified	Uncertain significance (Aug 04, 2022)
16-75112615-C-T		LDHD-related disorder	Benign (Dec 31, 2019)
16-75112631-C-G		LDHD-related disorder	Benign (May 21, 2018)
16-75112645-C-T		not specified	Uncertain significance (Oct 28, 2024)
16-75112646-G-A		not specified	Likely benign (Dec 15, 2023)
16-75112647-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-75112648-C-T		not specified	Uncertain significance (May 15, 2023)
16-75112657-G-C		not specified	Uncertain significance (Sep 01, 2021)
16-75112687-C-T		not specified	Uncertain significance (Sep 22, 2023)
16-75112702-C-G		not specified	Uncertain significance (Jan 02, 2024)
16-75112702-C-T		not specified	Uncertain significance (Mar 29, 2024)
16-75112843-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-75112873-C-T		not specified	Uncertain significance (Jan 26, 2023)
16-75112876-C-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDHD	protein_coding	protein_coding	ENST00000300051	11	4912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-13	0.0910	125640	0	106	125746	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.434	324	347	0.934	0.0000240	3218
Missense in Polyphen		102	131.82	0.77379		1216
Synonymous	-1.17	176	157	1.12	0.0000120	1096
Loss of Function	0.681	22	25.7	0.855	0.00000139	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000453	0.000449
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.000600	0.000598
Finnish	0.000296	0.000277
European (Non-Finnish)	0.000520	0.000510
Middle Eastern	0.000600	0.000598
South Asian	0.000201	0.000196
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Pyruvate metabolism - Homo sapiens (human);Pyruvate Dehydrogenase Complex Deficiency;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Leigh Syndrome;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Pyruvaldehyde Degradation;Pathways in clear cell renal cell carcinoma;Metabolism of proteins;Glycolysis Gluconeogenesis;Pyruvate metabolism;methylglyoxal degradation VI;Mitochondrial protein import;methylglyoxal degradation I;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.118
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.0598
• hipred: N
• hipred_score: 0.167
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldhd

Gene ontology

• Biological process: oxidation-reduction process;lactate catabolic process
• Cellular component: mitochondrion;mitochondrial inner membrane
• Molecular function: D-lactate dehydrogenase (cytochrome) activity;protein binding;D-lactate dehydrogenase activity;flavin adenine dinucleotide binding;FAD binding