ABHD16A

protein-coding

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

Gene summary

A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. The protein encoded by this gene is thought to be involved in some aspects of immunity. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

Previous symbols:

BAT5

MANE transcript

NM_021160.3

Inheritance

ClinVar variants

P:9U:78B:13

Top phenotype

Spastic paraplegia 86, autosomal recessive

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr6:31,686,955-31,703,356

External References & Databases

Ensembl (ENSG00000204427)

Transcript & Mutation Effects

hg38 • Region Span ~16.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spastic paraplegia 86, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030673

Submitter: PanelApp Australia

spastic paraplegia 86, autosomal recessiveMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030673

Submitter: Ambry Genetics

spastic paraplegia 86, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030673

Submitter: Labcorp Genetics (formerly Invitae)

spastic paraplegia 86, autosomal recessiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030673

Submitter: G2P

Clinical Genomic Database (CGD)

Spastic paraplegia 86, autosomal recessiveAR

Manifestation: Craniofacial; Neurologic

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

Refs: 34489854; 34587489; 34866177

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABHD16A variants in ClinVar

9 Conditions Cataloged

Inborn genetic diseasesTotal: 62

Spastic paraplegia 86, autosomal recessiveTotal: 14

not providedTotal: 12

Spastic paraplegiaTotal: 6

not specifiedTotal: 6

ABHD16A-related disorderTotal: 3

Complex hereditary spastic paraplegiaTotal: 2

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021160.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	3 clinvar	1 clinvar	7
missense	1 clinvar		66 clinvar	9 clinvar		76
nonsense	4 clinvar	2 clinvar				6
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	8 clinvar			9
Total	5	4	78	12	1	100

Highest pathogenic variant AF is 0.000013142677

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 73 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021160.3	RefSeq	NP_066983.1	20	MANE Select
ENST00000395952.8	Ensembl	ENSP00000379282.3	20	MANE Select
NM_001177515.2	RefSeq	NP_001170986.1	18	Standard
ENST00000440843.2	Ensembl	ENSP00000410347.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

monoacylglycerol catabolic process
prostaglandin catabolic process

Molecular Function

lysophospholipase activity
protein binding
acylglycerol lipase activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395952
Coding exons: 20
Length: 16496
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.48	207	335	0.619	0.0000204	3580
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000055	0.000054	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.000099	0.000097	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

RVIS EVS: -0.34
RVIS percentile EVS: 30.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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