ALDH1A2
Basic information
Region (hg38): 15:57953424-58497866
Links
Phenotypes
GenCC
Source:
- diaphragmatic hernia 4, with cardiovascular defects (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Diaphragmatic hernia 4, with cardiovascular defects | AR | Cardiovascular | The condition may involve complex cardiovascular anomalies, and awareness may allow early surgical and related management if indicated | Cardiovascular; Craniofacial; Musculoskeletal | 33565183 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALDH1A2 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 | 7 | |||||
missense | 17 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 1 | ||||
non coding | 30 | 31 | ||||
Total | 0 | 0 | 19 | 9 | 31 |
Variants in ALDH1A2
This is a list of pathogenic ClinVar variants found in the ALDH1A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-57955212-G-C | Likely benign (Mar 28, 2018) | |||
15-57955213-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
15-57955214-G-C | not specified | Uncertain significance (Oct 04, 2022) | ||
15-57955233-C-G | not specified | Uncertain significance (Apr 25, 2023) | ||
15-57955251-C-T | ALDH1A2-related disorder | Likely benign (Sep 01, 2024) | ||
15-57955365-C-G | Benign (Nov 10, 2018) | |||
15-57955467-AAAG-A | Benign (Jun 18, 2021) | |||
15-57960536-C-T | Benign (Jun 18, 2021) | |||
15-57960653-G-A | Benign (Jun 18, 2021) | |||
15-57960760-T-G | Benign (Dec 31, 2019) | |||
15-57960864-C-T | Benign (Nov 10, 2018) | |||
15-57960908-T-C | Benign (Nov 10, 2018) | |||
15-57961071-T-G | Benign (Nov 10, 2018) | |||
15-57961164-G-C | not specified | Uncertain significance (Apr 28, 2023) | ||
15-57961164-G-T | Diaphragmatic hernia 4, with cardiovascular defects | Pathogenic (Sep 01, 2022) | ||
15-57961292-G-T | ALDH1A2-related disorder | Benign (Dec 31, 2019) | ||
15-57961782-CTAA-C | Benign (Jun 18, 2021) | |||
15-57961980-T-A | Benign (Jun 18, 2021) | |||
15-57962028-C-T | Likely benign (Jul 30, 2018) | |||
15-57962046-T-C | Uncertain significance (Aug 01, 2024) | |||
15-57962063-C-T | Likely benign (Oct 01, 2024) | |||
15-57962116-C-T | Diaphragmatic hernia 4, with cardiovascular defects | Pathogenic (Sep 01, 2022) | ||
15-57962117-G-A | Likely benign (Apr 01, 2023) | |||
15-57962136-T-C | not specified | Uncertain significance (Feb 06, 2024) | ||
15-57962154-T-C | not specified | Uncertain significance (Jan 03, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ALDH1A2 | protein_coding | protein_coding | ENST00000249750 | 13 | 544444 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.363 | 0.637 | 125733 | 0 | 15 | 125748 | 0.0000596 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.44 | 215 | 283 | 0.759 | 0.0000153 | 3399 |
Missense in Polyphen | 83 | 146.21 | 0.56767 | 1799 | ||
Synonymous | -1.75 | 128 | 105 | 1.22 | 0.00000572 | 1010 |
Loss of Function | 3.69 | 6 | 26.5 | 0.226 | 0.00000130 | 325 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000152 | 0.000152 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000651 | 0.0000615 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Does metabolize octanal and decanal but does not metabolize citral, benzaldehyde, acetaldehyde and propanal efficiently (By similarity). {ECO:0000250}.;
- Pathway
- Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Ethanol effects on histone modifications;Tryptophan metabolism;Vitamin A and Carotenoid Metabolism;Signal Transduction;RA biosynthesis pathway;Lysine degradation;Propanoate metabolism;retinoate biosynthesis I;Pyruvate metabolism;Signaling by Retinoic Acid;Signaling by Nuclear Receptors;Tryptophan degradation;Valine Leucine Isoleucine degradation;Histidine degradation
(Consensus)
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- loftool
- 0.302
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24.33
Haploinsufficiency Scores
- pHI
- 0.423
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.490
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.835
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | High |
Mouse Genome Informatics
- Gene name
- Aldh1a2
- Phenotype
- craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; respiratory system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- aldh1a2
- Affected structure
- hyohyoideus
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- blood vessel development;kidney development;liver development;regulation of endothelial cell proliferation;heart morphogenesis;vitamin A metabolic process;midgut development;positive regulation of cell population proliferation;negative regulation of cell population proliferation;determination of bilateral symmetry;proximal/distal pattern formation;positive regulation of gene expression;neural crest cell development;morphogenesis of embryonic epithelium;neural tube development;pituitary gland development;neuron differentiation;lung development;hindbrain development;pancreas development;embryonic camera-type eye development;response to estradiol;response to vitamin A;response to cytokine;embryonic forelimb morphogenesis;ureter maturation;retinol metabolic process;retinoic acid metabolic process;retinal metabolic process;9-cis-retinoic acid biosynthetic process;positive regulation of apoptotic process;embryonic digestive tract development;cardiac muscle tissue development;oxidation-reduction process;face development;cellular response to retinoic acid;retinoic acid receptor signaling pathway involved in somitogenesis
- Cellular component
- cytoplasm;cytosol;perinuclear region of cytoplasm
- Molecular function
- retinal dehydrogenase activity;3-chloroallyl aldehyde dehydrogenase activity;aldehyde dehydrogenase (NAD) activity;retinal binding