ABHD16A

abhydrolase domain containing 16A, phospholipase, the group of Abhydrolase domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:31686955-31703356

Previous symbols: [ "BAT5" ]

Links

ENSG00000204427 ∙ NCBI:7920 ∙ OMIM:142620 ∙ HGNC:13921 ∙ Uniprot:O95870 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spastic paraplegia 86, autosomal recessive (Moderate), mode of inheritance: AR
• spastic paraplegia 86, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 86, autosomal recessive	AR	General	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	Craniofacial; Neurologic	34489854; 34587489; 34866177

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABHD16A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABHD16A 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				2	1	3
missense			30	6		36
nonsense			1			1
start loss						0
frameshift		1	1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				1		1
Total	0	1	32	9	1

Variants in ABHD16A

This is a list of pathogenic ClinVar variants found in the ABHD16A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31687253-G-A		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
6-31687518-G-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
6-31687532-C-T		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
6-31687660-C-T		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
6-31687687-G-A		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
6-31687723-A-G		ABHD16A-related disorder	Uncertain significance (Feb 07, 2023)
6-31687731-TA-T		Autosomal recessive complex spastic paraplegia	Likely pathogenic (Sep 30, 2021)
6-31687735-T-C		Inborn genetic diseases	Likely benign (Aug 12, 2021)
6-31687744-G-C		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
6-31687890-C-G		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
6-31687893-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
6-31688041-C-T		Complex hereditary spastic paraplegia • Spastic paraplegia 86, autosomal recessive	Pathogenic (Feb 09, 2022)
6-31688077-C-T		Inborn genetic diseases	Uncertain significance (May 01, 2022)
6-31688078-G-A		Spastic paraplegia	Uncertain significance (Jul 01, 2021)
6-31688237-C-CCACG			Likely benign (Feb 01, 2024)
6-31688737-C-T			Benign (Jul 01, 2024)
6-31688740-G-A			Likely benign (Feb 01, 2024)
6-31688747-A-C		Spastic paraplegia 86, autosomal recessive • Spastic paraplegia	Uncertain significance (Jul 01, 2021)
6-31689027-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
6-31690086-C-T		Inborn genetic diseases	Uncertain significance (Mar 19, 2024)
6-31691587-G-A		Spastic paraplegia 86, autosomal recessive	Pathogenic (Feb 09, 2022)
6-31691667-C-T		Spastic paraplegia	Uncertain significance (Jul 01, 2021)
6-31691671-G-A		Inborn genetic diseases	Uncertain significance (May 09, 2023)
6-31691680-A-T		Inborn genetic diseases	Uncertain significance (Apr 20, 2024)
6-31691890-G-A		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABHD16A	protein_coding	protein_coding	ENST00000395952	20	16496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.473	0.527	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	207	335	0.619	0.0000204	3580
Missense in Polyphen		55	110.56	0.49747		1186
Synonymous	1.02	110	124	0.884	0.00000659	1116
Loss of Function	4.63	9	41.0	0.220	0.00000232	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000212	0.000210
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000547	0.0000544
Finnish	0.000417	0.000416
European (Non-Finnish)	0.0000989	0.0000967
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000331	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.747
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abhd16a
• Phenotype: hematopoietic system phenotype; 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); homeostasis/metabolism phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: monoacylglycerol catabolic process;prostaglandin catabolic process
• Cellular component: integral component of membrane
• Molecular function: lysophospholipase activity;protein binding;acylglycerol lipase activity