GeneBe

ALDH3A2

protein-coding

aldehyde dehydrogenase 3 family member A2, the group of Aldehyde dehydrogenases

Gene summary

Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:
  • SLS
  • ALDH10

MANE transcript

NM_000382.3

Inheritance

AR

ClinVar variants

P:204U:137B:198

Top phenotype

Sjogren-Larsson syndrome

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr17:19,648,136-19,685,760

External References & Databases

Ensembl (ENSG00000072210)NCBI Gene (224)OMIM (609523)HGNC:403GenCCUniProt (P51648)AlphaFoldClinVar (ALDH3A2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~37.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Sjogren-Larsson syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: PanelApp Australia

Sjogren-Larsson syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: Natera

Sjogren-Larsson syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: Myriad Women's Health

Sjogren-Larsson syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: Labcorp Genetics (formerly Invitae)

Sjogren-Larsson syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: Orphanet

Sjogren-Larsson syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010031

Submitter: G2P

Clinical Genomic Database (CGD)

Sjogren-Larsson syndromeAR

Manifestation: Biochemical; Dermatologic; Neurologic; Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Medical treatment (eg, with Zileuton) may be beneficial for certain aspects

Refs: 13354244; 13457946; 8176565; 9027499; 9829906; 11124298; 11408337; 16476818; 21684788; 21872273; 22397046; 22426667; 22833178; 23034980; 25784589; 31512987Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ALDH3A2 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 483
Sjögren-Larsson syndromeTotal: 250
Inborn genetic diseasesTotal: 52
not specifiedTotal: 45
ALDH3A2-related disorderTotal: 21
Cerebral palsyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000382.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
5
clinvar
181
clinvar
 187
missense
6
clinvar
28
clinvar
126
clinvar
17
clinvar
 177
nonsense
17
clinvar
22
clinvar
 39
start loss
1
clinvar
4
clinvar
 5
frameshift
57
clinvar
40
clinvar
2
clinvar
 99
splice donor/acceptor (+/-2bp)
6
clinvar
22
clinvar
4
clinvar
 32
Total871171371980539

Highest pathogenic variant AF is 0.00009850996

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 86 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000382.3RefSeqNP_000373.110MANE Select
ENST00000176643.11EnsemblENSP00000176643.610MANE Select
NM_001031806.2RefSeqNP_001026976.110Standard
NM_001369136.1RefSeqNP_001356065.110Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • fatty acid alpha-oxidation
  • cellular aldehyde metabolic process
  • central nervous system development
  • peripheral nervous system development
  • epidermis development

Molecular Function

  • 3-chloroallyl aldehyde dehydrogenase activity
  • aldehyde dehydrogenase (NAD) activity
  • protein binding
  • protein homodimerization activity
  • glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity

Cellular Component

  • peroxisomal membrane
  • endoplasmic reticulum membrane
  • integral component of membrane
  • intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000339618
Coding exons
10
Length
29463
Individuals with no LoFs
125681
Homozygous LoFs
0
Heterozygous LoFs
67
Defined
125748
p
0.000266
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6822452770.8850.00001513313
Missense (PolyPhen)6394.2040.668761141
Synonymous1.53851050.8100.000005971007
Loss of Function2.211223.60.5090.00000111293

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.000750.00075rare
Ashkenazi Jewish00.0absent
East Asian0.000220.00022rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000240.00024rare
South Asian0.000160.00016rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acids. Active on a variety of saturated and unsaturated aliphatic aldehydes between 6 and 24 carbons in length (PubMed:9133646, PubMed:22633490, PubMed:25047030). Responsible for conversion of the sphingosine 1-phosphate (S1P) degradation product hexadecenal to hexadecenoic acid (PubMed:22633490). {ECO:0000269|PubMed:22633490, ECO:0000269|PubMed:25047030, ECO:0000269|PubMed:9133646}.;

Recessive Scores

pRec
0.338

Intolerance Scores

LoFtool
0.251
RVIS EVS
-0.11
RVIS percentile EVS
45.36

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.397

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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