ALDH9A1

aldehyde dehydrogenase 9 family member A1, the group of Aldehyde dehydrogenases

Basic information

Region (hg38): 1:165662216-165698562

Previous symbols: [ "ALDH7", "ALDH4", "ALDH9" ]

Links

ENSG00000143149 ∙ NCBI:223 ∙ OMIM:602733 ∙ HGNC:412 ∙ Uniprot:P49189 ∙ 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 ALDH9A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH9A1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in ALDH9A1

This is a list of pathogenic ClinVar variants found in the ALDH9A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-165663115-T-C		not specified	Uncertain significance (Aug 30, 2022)
1-165663123-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-165663127-C-T		not specified	Uncertain significance (May 24, 2024)
1-165663139-C-G		not specified	Uncertain significance (Oct 05, 2021)
1-165667348-T-C		not specified	Uncertain significance (Jan 08, 2024)
1-165667380-A-C		not specified	Uncertain significance (Dec 19, 2022)
1-165667393-G-A		not specified	Uncertain significance (Apr 28, 2023)
1-165667395-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-165668955-T-C		not specified	Uncertain significance (Jun 11, 2021)
1-165668976-G-T		not specified	Uncertain significance (Jun 04, 2024)
1-165668986-T-G		not specified	Likely benign (Feb 03, 2022)
1-165669291-G-C		not specified	Uncertain significance (Sep 13, 2023)
1-165669296-C-T		not specified	Uncertain significance (May 23, 2024)
1-165669414-C-G		not specified	Uncertain significance (Dec 14, 2022)
1-165669450-C-A			Uncertain significance (Nov 01, 2023)
1-165679462-T-C		not specified	Uncertain significance (May 26, 2024)
1-165679552-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-165680534-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-165680547-C-T			Likely benign (Apr 01, 2022)
1-165680569-C-T		not specified	Uncertain significance (Apr 20, 2024)
1-165680635-A-G		not specified	Uncertain significance (May 24, 2024)
1-165682109-C-G		not specified	Uncertain significance (Apr 21, 2022)
1-165682137-A-G		not specified	Uncertain significance (Dec 15, 2023)
1-165682149-A-C		not specified	Uncertain significance (Jan 30, 2024)
1-165682151-G-A		not specified	Uncertain significance (Oct 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALDH9A1	protein_coding	protein_coding	ENST00000354775	11	36648

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-11	0.296	125619	0	129	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	312	292	1.07	0.0000144	3352
Missense in Polyphen		117	110.34	1.0603		1297
Synonymous	-0.856	119	108	1.10	0.00000563	1029
Loss of Function	1.01	20	25.5	0.783	0.00000141	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000388
Ashkenazi Jewish	0.00	0.00
East Asian	0.000403	0.000381
Finnish	0.00147	0.00143
European (Non-Finnish)	0.000698	0.000668
Middle Eastern	0.000403	0.000381
South Asian	0.000105	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts gamma-trimethylaminobutyraldehyde into gamma- butyrobetaine. Catalyzes the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction. {ECO:0000269|PubMed:10702312}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Pyruvate metabolism - Homo sapiens (human);Arginine and proline metabolism - Homo sapiens (human);Glycolysis / Gluconeogenesis - Homo sapiens (human);Glycerolipid metabolism - Homo sapiens (human);beta-Alanine metabolism - Homo sapiens (human);Lysine degradation - Homo sapiens (human);Histidine metabolism - Homo sapiens (human);Fatty acid degradation - Homo sapiens (human);Ascorbate and aldarate metabolism - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Carnitine Synthesis;GABA receptor Signaling;Tryptophan metabolism;Branched-chain amino acid catabolism;Glutamate Glutamine metabolism;Metabolism of amino acids and derivatives;Tyrosine metabolism;Glycolysis and Gluconeogenesis;Leukotriene metabolism;Metabolism;Lysine degradation;Propanoate metabolism;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;Arginine Proline metabolism;Carnitine synthesis;Pyruvate metabolism;Tryptophan degradation;L-carnitine biosynthesis;Valine Leucine Isoleucine degradation;Histidine degradation;Validated targets of C-MYC transcriptional repression (Consensus)

Recessive Scores

• pRec: 0.247

Intolerance Scores

• loftool: 0.405
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.0437
• hipred: N
• hipred_score: 0.289
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aldh9a1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular aldehyde metabolic process;neurotransmitter biosynthetic process;hormone metabolic process;carnitine biosynthetic process;oxidation-reduction process
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: 3-chloroallyl aldehyde dehydrogenase activity;aldehyde dehydrogenase (NAD) activity;aminobutyraldehyde dehydrogenase activity;1-pyrroline dehydrogenase activity;glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity;4-trimethylammoniobutyraldehyde dehydrogenase activity