ABHD14A-ACY1

ABHD14A-ACY1 readthrough

Basic information

Region (hg38): 3:51974705-51989183

Links

ENSG00000114786 ∙ NCBI:100526760 ∙ ∙ HGNC:38856 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABHD14A-ACY1 gene.

• not provided (105 variants)
• Inborn genetic diseases (40 variants)
• Aminoacylase 1 deficiency (24 variants)
• not specified (7 variants)
• Intellectual disability (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD14A-ACY1 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			3	25	1	29
missense	1	1	65	12		79
nonsense			1			1
start loss						0
frameshift	2	2	2			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2		4	6	1	13
splice region						0
non coding			8	8	7	23
Total	5	3	84	51	9

Highest pathogenic variant AF is 0.0000131

Variants in ABHD14A-ACY1

This is a list of pathogenic ClinVar variants found in the ABHD14A-ACY1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-51975142-G-T		not specified	Uncertain significance (Jul 25, 2023)
3-51975164-T-G		not specified	Uncertain significance (Jan 08, 2024)
3-51975197-T-G		not specified	Uncertain significance (Dec 16, 2022)
3-51975203-C-G		not specified	Uncertain significance (Apr 12, 2022)
3-51977880-C-G		not specified	Uncertain significance (Dec 20, 2023)
3-51977916-G-C		not specified	Uncertain significance (Mar 14, 2023)
3-51977925-C-G		not specified	Uncertain significance (Nov 17, 2023)
3-51977934-A-G		not specified	Uncertain significance (Jan 03, 2022)
3-51977962-G-A		not specified	Uncertain significance (Aug 22, 2023)
3-51978001-A-G		not specified	Uncertain significance (Aug 04, 2021)
3-51978071-C-G		not specified	Uncertain significance (Nov 08, 2022)
3-51978310-G-T		not specified	Uncertain significance (Oct 04, 2022)
3-51978314-C-G		not specified	Uncertain significance (Oct 17, 2023)
3-51978353-G-C		not specified	Uncertain significance (Jan 24, 2023)
3-51978356-G-A		not specified	Uncertain significance (Dec 28, 2022)
3-51980441-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-51980462-C-T		not specified	Likely benign (Jan 10, 2023)
3-51980578-G-C		not specified	Uncertain significance (Oct 13, 2023)
3-51980879-C-T		not specified	Uncertain significance (Nov 17, 2022)
3-51980882-G-A		not specified	Uncertain significance (Jan 10, 2023)
3-51980893-C-T		not specified	Uncertain significance (Sep 25, 2023)
3-51980902-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-51980915-A-G		not specified	Uncertain significance (Jul 25, 2023)
3-51980936-G-C		not specified	Uncertain significance (Feb 16, 2023)
3-51980957-A-G		not specified	Uncertain significance (Feb 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD14A-ACY1	protein_coding	protein_coding	ENST00000463937	16	14134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.77e-10	0.615	125600	0	148	125748	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.237	274	285	0.960	0.0000176	3272
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00182	0.00181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00229	0.00229
Finnish	0.0000960	0.0000924
European (Non-Finnish)	0.000468	0.000466
Middle Eastern	0.00229	0.00229
South Asian	0.000329	0.000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Arginine biosynthesis - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.0814
• hipred: N
• hipred_score: 0.132
• ghis: 0.470

Gene Damage Prediction

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

Gene ontology

• Biological process: proteolysis;cellular amino acid metabolic process
• Cellular component: cytoplasm
• Molecular function: aminoacylase activity;metallopeptidase activity