ALDH3A1

aldehyde dehydrogenase 3 family member A1, the group of Aldehyde dehydrogenases

Basic information

Region (hg38): 17:19737984-19748943

Previous symbols: [ "ALDH3" ]

Links

ENSG00000108602

∙ NCBI:218 ∙ OMIM:100660 ∙ HGNC:405 ∙ Uniprot:P30838 ∙ 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 ALDH3A1 gene.

not_specified (36 variants)
not_provided (8 variants)
Keratoconus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH3A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000691.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	4 clinvar	5
missense		1 clinvar	37 clinvar	3 clinvar	1 clinvar	42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	38	4	5

Highest pathogenic variant AF is 0.000033461685

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALDH3A1	protein_coding	protein_coding	ENST00000457500	10	10960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.90e-17	0.00288	125474	1	273	125748	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.295	273	287	0.951	0.0000175	2940
Missense in Polyphen		85	102.07	0.83277		1135
Synonymous	-0.583	137	129	1.07	0.00000900	884
Loss of Function	-0.397	24	22.0	1.09	0.00000102	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00321	0.00321
Ashkenazi Jewish	0.00	0.00
East Asian	0.000495	0.000489
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00106	0.00105
Middle Eastern	0.000495	0.000489
South Asian	0.000753	0.000752
Other	0.00261	0.00261

dbNSFP

Source: dbNSFP

Function: FUNCTION: ALDHs play a major role in the detoxification of alcohol-derived acetaldehyde (Probable). They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation (Probable). Oxidizes medium and long chain aldehydes into non-toxic fatty acids (PubMed:1737758). Preferentially oxidizes aromatic aldehyde substrates (PubMed:1737758). Comprises about 50 percent of corneal epithelial soluble proteins (By similarity). May play a role in preventing corneal damage caused by ultraviolet light (By similarity). {ECO:0000250|UniProtKB:P47739, ECO:0000269|PubMed:1737758, ECO:0000305}.;
Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Phenylalanine metabolism - Homo sapiens (human);Histidine metabolism - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);Cyclophosphamide Pathway, Pharmacodynamics;Ifosfamide Pathway, Pharmacodynamics;Tyrosinemia, transient, of the newborn;Dopamine beta-hydroxylase deficiency;Disulfiram Action Pathway;Histidine Metabolism;Familial lipoprotein lipase deficiency;Tyrosine Metabolism;Alkaptonuria;Monoamine oxidase-a deficiency (MAO-A);Hawkinsinuria;Tyrosinemia Type I;Histidinemia;Felbamate Metabolism Pathway;Glycerolipid Metabolism;Cyclophosphamide Action Pathway;Ifosfamide Action Pathway;Glycerol Kinase Deficiency;D-glyceric acidura;Cyclophosphamide Metabolism Pathway;Ifosfamide Metabolism Pathway;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Phase I - Functionalization of compounds;Tyrosine metabolism;Glycolysis and Gluconeogenesis;Leukotriene metabolism;Biological oxidations;Metabolism;Phenylalanine degradation;2,-deoxy-α-D-ribose 1-phosphate degradation;Histidine metabolism;Lysine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Valine, leucine and isoleucine degradation;Bile acid biosynthesis;Glycerophospholipid metabolism;Xenobiotics metabolism;Tyrosine metabolism;Histidine degradation;putrescine degradation III (Consensus)

Intolerance Scores

loftool: 0.313
rvis_EVS: 0.11
rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

pHI: 0.390
hipred: N
hipred_score: 0.208
ghis: 0.378

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Aldh3a1
Phenotype: growth/size/body region phenotype; skeleton phenotype; normal phenotype;

Gene ontology

Biological process: cellular aldehyde metabolic process;xenobiotic metabolic process;oxidation-reduction process
Cellular component: extracellular space;endoplasmic reticulum;cytosol;plasma membrane;integral component of membrane
Molecular function: 3-chloroallyl aldehyde dehydrogenase activity;aldehyde dehydrogenase (NAD) activity;aldehyde dehydrogenase [NAD(P)+] activity;protein binding;alcohol dehydrogenase (NADP+) activity;benzaldehyde dehydrogenase (NAD+) activity