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.

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.

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	4	5
missense			19	3	1	23
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	4	5

Variants in ALDH3A1

This is a list of pathogenic ClinVar variants found in the ALDH3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-19739031-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-19739549-C-T		not specified	Uncertain significance (Jun 06, 2023)
17-19739598-G-A			Likely benign (Apr 16, 2018)
17-19739638-G-A		not specified	Uncertain significance (Aug 17, 2022)
17-19739644-T-G		not specified	Uncertain significance (Aug 12, 2021)
17-19740351-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-19740352-G-A			Benign (Jul 07, 2018)
17-19740360-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-19740386-C-T			Benign (Jul 27, 2018)
17-19740426-T-C		not specified	Uncertain significance (Sep 23, 2023)
17-19741136-G-C		not specified	Uncertain significance (Jan 26, 2022)
17-19741197-C-T		Keratoconus	Likely pathogenic (Feb 25, 2023)
17-19741203-C-T			Likely benign (Jul 07, 2018)
17-19742052-T-C		not specified	Uncertain significance (Jan 25, 2024)
17-19742070-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-19742099-C-T			Benign (Aug 04, 2018)
17-19742133-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-19742172-G-A		not specified	Uncertain significance (May 30, 2023)
17-19742209-G-C		not specified	Uncertain significance (Jan 17, 2024)
17-19742609-G-A		not specified	Uncertain significance (Aug 30, 2021)
17-19742610-G-A		not specified	Uncertain significance (May 20, 2024)
17-19743244-C-A		not specified	Uncertain significance (May 26, 2023)
17-19743264-G-A		not specified	Uncertain significance (Sep 15, 2021)
17-19743368-G-A			Benign (Apr 04, 2018)
17-19744989-C-T			Benign (Aug 04, 2018)

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