ALDH1L2

aldehyde dehydrogenase 1 family member L2, the group of Aldehyde dehydrogenases

Basic information

Region (hg38): 12:105019784-105107643

Links

ENSG00000136010 ∙ NCBI:160428 ∙ OMIM:613584 ∙ HGNC:26777 ∙ Uniprot:Q3SY69 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALDH1L2 gene.

• not_specified (74 variants)
• Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH1L2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001034173.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			71	4		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALDH1L2	protein_coding	protein_coding	ENST00000258494	23	64788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-17	0.733	125336	2	410	125748	0.00164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	414	500	0.828	0.0000254	6035
Missense in Polyphen		157	210.84	0.74464		2535
Synonymous	0.929	167	183	0.913	0.0000102	1776
Loss of Function	2.00	34	49.1	0.692	0.00000240	607

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00419	0.00420
Ashkenazi Jewish	0.00238	0.00238
East Asian	0.00180	0.00180
Finnish	0.000648	0.000647
European (Non-Finnish)	0.00187	0.00185
Middle Eastern	0.00180	0.00180
South Asian	0.00131	0.00127
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

• Pathway: One carbon pool by folate - Homo sapiens (human);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: 0.104

Intolerance Scores

• loftool: 0.839
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.24

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.394
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aldh1l2

Gene ontology

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