LDHAL6A

lactate dehydrogenase A like 6A

Basic information

Region (hg38): 11:18455824-18479601

Links

ENSG00000166800 ∙ NCBI:160287 ∙ OMIM:618928 ∙ HGNC:28335 ∙ Uniprot:Q6ZMR3 ∙ 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 LDHAL6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDHAL6A 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in LDHAL6A

This is a list of pathogenic ClinVar variants found in the LDHAL6A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18456706-T-C		not specified	Uncertain significance (Aug 15, 2023)
11-18456763-C-A		not specified	Uncertain significance (Mar 31, 2023)
11-18465640-A-G		not specified	Uncertain significance (Jan 09, 2024)
11-18465661-A-G		not specified	Uncertain significance (Sep 25, 2023)
11-18465700-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-18475523-T-C		not specified	Uncertain significance (Feb 17, 2024)
11-18475600-T-G		not specified	Uncertain significance (May 30, 2022)
11-18475604-A-G		not specified	Uncertain significance (Aug 11, 2022)
11-18475637-G-C		not specified	Uncertain significance (Feb 06, 2024)
11-18475638-T-G		not specified	Uncertain significance (Jan 30, 2024)
11-18476410-G-A		not specified	Uncertain significance (Aug 26, 2022)
11-18476444-T-A		not specified	Uncertain significance (Dec 16, 2023)
11-18477715-G-C		not specified	Uncertain significance (Dec 28, 2022)
11-18478707-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-18478718-A-G		not specified	Uncertain significance (Jan 22, 2024)
11-18478778-C-T		not specified	Uncertain significance (May 11, 2022)
11-18478794-T-G		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDHAL6A	protein_coding	protein_coding	ENST00000280706	7	23777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.78e-10	0.0524	125480	0	259	125739	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.272	170	180	0.943	0.00000900	2193
Missense in Polyphen		56	63.027	0.8885		885
Synonymous	-0.991	72	62.1	1.16	0.00000307	634
Loss of Function	-0.217	14	13.2	1.06	6.36e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00167	0.00167
Ashkenazi Jewish	0.000603	0.000595
East Asian	0.000109	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.00161	0.00160
Middle Eastern	0.000109	0.000109
South Asian	0.000534	0.000523
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays an lactate dehydrogenase activity. Significantly increases the transcriptional activity of JUN, when overexpressed. {ECO:0000269|PubMed:18351441}.
• 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);Beta-mercaptolactate-cysteine disulfiduria;Warburg Effect;Pyruvate Dehydrogenase Complex Deficiency;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Gluconeogenesis;Leigh Syndrome;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Cysteine Metabolism;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Cystinosis, ocular nonnephropathic;Glycogenosis, Type IB;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;lactate fermentation (reoxidation of cytosolic NADH);The citric acid (TCA) cycle and respiratory electron transport;Metabolism (Consensus)

Recessive Scores

• pRec: 0.483

Intolerance Scores

• loftool: 0.423
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.0854
• hipred: N
• hipred_score: 0.242
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Gene ontology

• Biological process: carbohydrate metabolic process;carboxylic acid metabolic process;oxidation-reduction process
• Cellular component: cytoplasm;extracellular exosome
• Molecular function: L-lactate dehydrogenase activity