ALDH1L1

aldehyde dehydrogenase 1 family member L1, the group of Aldehyde dehydrogenases

Basic information

Region (hg38): 3:126103562-126197994

Previous symbols: [ "FTHFD" ]

Links

ENSG00000144908 ∙ NCBI:10840 ∙ OMIM:600249 ∙ HGNC:3978 ∙ Uniprot:O75891 ∙ 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 ALDH1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH1L1 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				4	4	8
missense			56	1	4	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	56	5	9

Variants in ALDH1L1

This is a list of pathogenic ClinVar variants found in the ALDH1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126105752-T-C		not specified	Uncertain significance (Sep 15, 2021)
3-126105771-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-126105794-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-126105876-C-A			Benign (Aug 16, 2018)
3-126105912-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-126107135-C-T			Benign (Jan 02, 2019)
3-126107145-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-126109950-G-A		not specified	Uncertain significance (May 23, 2023)
3-126109957-C-T			Benign (Dec 31, 2019)
3-126109980-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-126110096-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-126112807-A-G		not specified	Uncertain significance (Jul 15, 2021)
3-126112858-T-A		not specified	Uncertain significance (Jan 17, 2024)
3-126114595-T-C		not specified	Uncertain significance (May 13, 2022)
3-126114640-C-T		not specified	Uncertain significance (Jul 14, 2021)
3-126114649-T-C		not specified	Uncertain significance (Apr 25, 2023)
3-126124406-C-G		not specified	Uncertain significance (Mar 30, 2024)
3-126125624-G-T		not specified	Uncertain significance (Sep 22, 2023)
3-126125630-T-G		not specified	Uncertain significance (Jun 27, 2022)
3-126125636-C-T		not specified	Uncertain significance (Apr 12, 2024)
3-126125666-T-C		not specified	Uncertain significance (Jan 26, 2022)
3-126125677-A-G		not specified	Uncertain significance (Jun 24, 2022)
3-126131415-C-T		not specified	Uncertain significance (May 18, 2023)
3-126131421-G-A		not specified	Uncertain significance (May 10, 2022)
3-126131421-G-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALDH1L1	protein_coding	protein_coding	ENST00000273450	23	94426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-11	0.997	125530	4	214	125748	0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.605	512	552	0.928	0.0000332	5937
Missense in Polyphen		228	247.55	0.92102		2559
Synonymous	-0.290	241	235	1.02	0.0000161	1811
Loss of Function	2.76	25	45.0	0.556	0.00000226	524

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000886	0.000877
Ashkenazi Jewish	0.000204	0.000198
East Asian	0.00143	0.00136
Finnish	0.00539	0.00486
European (Non-Finnish)	0.000494	0.000475
Middle Eastern	0.00143	0.00136
South Asian	0.000342	0.000327
Other	0.000516	0.000489

dbNSFP

Source: dbNSFP

• Pathway: One carbon pool by folate - Homo sapiens (human);Folate malabsorption, hereditary;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Methotrexate Action Pathway;Folate Metabolism;Folate-Alcohol and Cancer Pathway Hypotheses;One Carbon Metabolism;Folate metabolism;Metabolism;folate transformations I;Metabolism of folate and pterines;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.199

Intolerance Scores

• loftool: 0.690
• rvis_EVS: -0.16
• rvis_percentile_EVS: 40.68

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.527
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.831

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aldh1l1
• Phenotype: hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: aldh1l1
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: accumulation

Gene ontology

• Biological process: one-carbon metabolic process;biosynthetic process;10-formyltetrahydrofolate catabolic process;folic acid metabolic process;oxidation-reduction process
• Cellular component: cytosol;extracellular exosome
• Molecular function: catalytic activity;aldehyde dehydrogenase (NAD) activity;formyltetrahydrofolate dehydrogenase activity;hydroxymethyl-, formyl- and related transferase activity