LDHAL6B

lactate dehydrogenase A like 6B

Basic information

Region (hg38): 15:59206843-59208588

Previous symbols: [ "LDHAL6" ]

Links

ENSG00000171989 ∙ NCBI:92483 ∙ ∙ HGNC:21481 ∙ Uniprot:Q9BYZ2 ∙ 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 LDHAL6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDHAL6B 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	31	2	1

Variants in LDHAL6B

This is a list of pathogenic ClinVar variants found in the LDHAL6B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59206966-G-A		not specified	Uncertain significance (Mar 15, 2023)
15-59207007-T-C		not specified	Uncertain significance (Feb 23, 2023)
15-59207041-C-T		not specified	Uncertain significance (May 13, 2024)
15-59207047-T-C		not specified	Uncertain significance (May 31, 2024)
15-59207048-C-G		not specified	Uncertain significance (Mar 31, 2024)
15-59207056-A-G		not specified	Uncertain significance (Jan 22, 2024)
15-59207061-A-T		not specified	Uncertain significance (Sep 29, 2022)
15-59207074-C-T		not specified	Uncertain significance (Jan 26, 2023)
15-59207118-C-T		not specified	Uncertain significance (Oct 27, 2021)
15-59207125-C-A		not specified	Uncertain significance (Jul 12, 2023)
15-59207164-T-C		not specified	Uncertain significance (Oct 25, 2023)
15-59207170-C-A		not specified	Uncertain significance (Jan 03, 2024)
15-59207170-C-G		not specified	Uncertain significance (Aug 08, 2022)
15-59207252-A-T		not specified	Uncertain significance (Jun 11, 2024)
15-59207287-A-G		not specified	Uncertain significance (Feb 28, 2024)
15-59207289-G-A		not specified	Uncertain significance (May 27, 2022)
15-59207293-G-A		not specified	Uncertain significance (Jul 06, 2021)
15-59207296-C-G		not specified	Uncertain significance (Jan 08, 2024)
15-59207307-A-C		not specified	Uncertain significance (Sep 16, 2021)
15-59207344-C-T		not specified	Uncertain significance (Nov 07, 2022)
15-59207376-G-A		not specified	Uncertain significance (Jun 07, 2024)
15-59207382-C-T		not specified	Uncertain significance (Jun 17, 2024)
15-59207415-G-C		Focal segmental glomerulosclerosis 6	Likely benign (Mar 26, 2020)
15-59207472-C-T		not specified	Uncertain significance (Feb 07, 2023)
15-59207554-A-G		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDHAL6B	protein_coding	protein_coding	ENST00000307144	1	1664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0734	0.758	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	263	218	1.21	0.0000128	2508
Missense in Polyphen		90	72.839	1.2356		973
Synonymous	-2.41	110	82.2	1.34	0.00000513	758
Loss of Function	0.971	2	4.13	0.484	2.62e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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);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: 0.419

Intolerance Scores

• loftool: 0.348
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.18

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: N
• hipred_score: 0.166

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ldhal6b

Gene ontology

• Biological process: carbohydrate metabolic process;pyruvate metabolic process;oxidation-reduction process
• Cellular component: nucleus;mitochondrial matrix
• Molecular function: L-lactate dehydrogenase activity;protein binding