ALDH1A1

aldehyde dehydrogenase 1 family member A1, the group of Aldehyde dehydrogenases

Basic information

Region (hg38): 9:72900670-73080442

Previous symbols: [ "PUMB1", "ALDH1" ]

Links

ENSG00000165092 ∙ NCBI:216 ∙ OMIM:100640 ∙ HGNC:402 ∙ Uniprot:P00352 ∙ 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 ALDH1A1 gene.

• Inborn genetic diseases (12 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH1A1 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		1
missense			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	11	2	1

Variants in ALDH1A1

This is a list of pathogenic ClinVar variants found in the ALDH1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-72901270-C-A		not specified	Uncertain significance (Oct 27, 2021)
9-72909635-G-C		not specified	Uncertain significance (Jun 18, 2021)
9-72909651-T-C		not specified	Uncertain significance (Jul 21, 2021)
9-72911950-C-A			Benign (Jul 18, 2018)
9-72911992-T-C		not specified	Uncertain significance (Jan 22, 2024)
9-72912034-C-A		not specified	Uncertain significance (Nov 29, 2023)
9-72912037-G-A		not specified	Uncertain significance (Oct 13, 2023)
9-72912074-T-C		not specified	Uncertain significance (Jan 04, 2024)
9-72916993-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-72917012-T-C		not specified	Uncertain significance (Jan 23, 2024)
9-72917017-T-A		not specified	Uncertain significance (Feb 23, 2023)
9-72924048-C-T		not specified	Uncertain significance (Oct 05, 2023)
9-72924099-G-A		not specified	Uncertain significance (Jul 21, 2021)
9-72925477-G-T			Benign (Jul 16, 2018)
9-72925567-G-T		not specified	Uncertain significance (Jul 12, 2023)
9-72925587-A-G		not specified	Uncertain significance (Nov 02, 2023)
9-72927161-T-C			Likely benign (Apr 03, 2018)
9-72927164-A-T			Benign (Aug 21, 2018)
9-72927171-T-A		not specified	Uncertain significance (Oct 02, 2023)
9-72928906-C-T		not specified	Uncertain significance (May 25, 2022)
9-72928943-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-72929012-A-T		not specified	Uncertain significance (Aug 02, 2021)
9-72931006-T-A		not specified	Uncertain significance (Oct 06, 2023)
9-72940166-C-G		not specified	Uncertain significance (May 17, 2023)
9-72952984-G-A		not specified	Likely benign (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALDH1A1	protein_coding	protein_coding	ENST00000297785	13	179781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0455	125731	0	8	125739	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	199	276	0.720	0.0000142	3260
Missense in Polyphen		57	116.85	0.4878		1421
Synonymous	-0.340	106	102	1.04	0.00000561	969
Loss of Function	4.13	4	27.3	0.146	0.00000130	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can convert/oxidize retinaldehyde to retinoic acid. Binds free retinal and cellular retinol-binding protein-bound retinal (By similarity). May have a broader specificity and oxidize other aldehydes in vivo (PubMed:19296407, PubMed:26373694, PubMed:25450233). {ECO:0000250|UniProtKB:P51647, ECO:0000269|PubMed:19296407, ECO:0000269|PubMed:25450233, ECO:0000269|PubMed:26373694}.
• Pathway: Retinol metabolism - Homo sapiens (human);Cyclophosphamide Pathway, Pharmacodynamics;Ifosfamide Pathway, Pharmacokinetics;Ifosfamide Pathway, Pharmacodynamics;Cyclophosphamide Action Pathway;Ifosfamide Action Pathway;Vitamin A Deficiency;Nevirapine Metabolism Pathway;Cyclophosphamide Metabolism Pathway;Ifosfamide Metabolism Pathway;Retinol Metabolism;Folate-Alcohol and Cancer Pathway Hypotheses;Fatty Acid Omega Oxidation;Dopaminergic Neurogenesis;Amino Acid metabolism;Ethanol effects on histone modifications;Tryptophan metabolism;Vitamin A and Carotenoid Metabolism;Signal Transduction;Phase I - Functionalization of compounds;RA biosynthesis pathway;Fructose metabolism;Metabolism of carbohydrates;Glutamate Glutamine metabolism;Ethanol oxidation;Biological oxidations;Metabolism;Lysine degradation;Propanoate metabolism;retinoate biosynthesis I;Arginine Proline metabolism;Pyruvate metabolism;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;Tryptophan degradation;Fructose catabolism;Valine Leucine Isoleucine degradation;Histidine degradation (Consensus)

Recessive Scores

• pRec: 0.386

Intolerance Scores

• loftool: 0.271
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.384
• hipred: Y
• hipred_score: 0.626
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.880

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aldh1a7

Gene ontology

• Biological process: retinoid metabolic process;ethanol oxidation;cellular aldehyde metabolic process;retinol metabolic process;positive regulation of GTPase activity;oxidation-reduction process;fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate;negative regulation of cold-induced thermogenesis
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: retinal dehydrogenase activity;aldehyde dehydrogenase (NAD) activity;GTPase activator activity;androgen binding;benzaldehyde dehydrogenase (NAD+) activity;NAD binding