ALDH16A1

protein-coding

aldehyde dehydrogenase 16 family member A1, the group of Aldehyde dehydrogenases

Gene summary

This gene encodes a member of the aldehyde dehydrogenase superfamily. The family members act on aldehyde substrates and use nicotinamide adenine dinucleotide phosphate (NADP) as a cofactor. This gene is conserved in chimpanzee, dog, cow, mouse, rat, and zebrafish. The protein encoded by this gene interacts with maspardin, a protein that when truncated is responsible for Mast syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

MANE transcript

NM_153329.4

Inheritance

—

ClinVar variants

U:111B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr19:49,453,225-49,471,050

External References & Databases

Ensembl (ENSG00000161618)

Transcript & Mutation Effects

hg38 • Region Span ~17.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ALDH16A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153329.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			8 clinvar	5 clinvar		13
missense			99 clinvar	7 clinvar		106
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	111	12	0	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153329.4	RefSeq	NP_699160.2	17	MANE Select
ENST00000293350.9	Ensembl	ENSP00000293350.3	17	MANE Select
NM_001145396.2	RefSeq	NP_001138868.1	16	Standard
ENST00000455361.6	Ensembl	ENSP00000410142.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

oxidation-reduction process

Molecular Function

oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

Cellular Component

membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293350
Coding exons: 17
Length: 17880
Individuals with no LoFs: 125639
Homozygous LoFs: 0
Heterozygous LoFs: 109
Defined: 125748
p: 0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.422	530	503	1.05	0.0000332	4943
Missense (PolyPhen)		197	202.57	0.97251		2106
Synonymous	0.0319	228	229	0.997	0.0000160	1805
Loss of Function	1.15	35	43.1	0.812	0.00000248	412

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00074	0.00072	rare
Ashkenazi Jewish	0.00051	0.00050	rare
East Asian	0.0010	0.0010	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00047	0.00046	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.832
RVIS EVS: 0.44
RVIS percentile EVS: 77.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.722

Gene Damage Prediction

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