ABHD14A-ACY1

protein-coding

ABHD14A-ACY1 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring abhydrolase domain containing 14A (ABHD14A) and aminoacylase 1 (ACY1) genes on chromosome 3. The read-through transcript encodes a protein that shares sequence identity with the downstream gene product but its N-terminal region is distinct due to the use of an alternate start codon relative to the upstream gene. [provided by RefSeq, Oct 2015]

MANE transcript

N/A

Inheritance

—

ClinVar variants

P:8U:75B:45

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr3:51,974,706-51,989,183

External References & Databases

Ensembl (ENSG00000114786)

NCBI Gene (100526760)

HGNC:38856

GenCC

ClinVar (ABHD14A-ACY1)

Transcript & Mutation Effects

hg38 • Region Span ~14.5 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 ABHD14A-ACY1 variants in ClinVar

5 Conditions Cataloged

not providedTotal: 105

Inborn genetic diseasesTotal: 40

Aminoacylase 1 deficiencyTotal: 24

not specifiedTotal: 7

Intellectual disabilityTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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			3 clinvar	25 clinvar	1 clinvar	29
missense	1 clinvar	1 clinvar	65 clinvar	12 clinvar		79
nonsense			1 clinvar			1
start loss						0
frameshift	2 clinvar	2 clinvar	2 clinvar			6
splice donor/acceptor (+/-2bp)	2 clinvar		4 clinvar	6 clinvar	1 clinvar	13
Total	5	3	75	43	2	128

Highest pathogenic variant AF is 0.0000131432

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001316331.2	RefSeq	NP_001303260.1	16	Standard
ENST00000463721.5	Ensembl	ENSP00000417688.1	4	Standard
ENST00000463937.1	Ensembl	ENSP00000420487.1	16	Standard
ENST00000486081.6	Ensembl	ENSP00000420395.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Arginine biosynthesis - Homo sapiens (human)

Biological Process

proteolysis
cellular amino acid metabolic process

Molecular Function

aminoacylase activity
metallopeptidase activity

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000463937
Coding exons: 16
Length: 14134
Individuals with no LoFs: 125600
Homozygous LoFs: 0
Heterozygous LoFs: 148
Defined: 125748
p: 0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.237	274	285	0.960	0.0000176	3272
Missense (PolyPhen)		110	130.04	0.84588		1472
Synonymous	0.443	108	114	0.947	0.00000687	1056
Loss of Function	1.36	19	26.6	0.715	0.00000117	310

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0023	0.0023	notable
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00033	0.00033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Gene Damage Prediction

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