ABHD16A

Chr 6AR

abhydrolase domain containing 16A, phospholipase

Also known as: BAT5, D6S82E, NG26, PP199, SPG86, hBAT5

NCBI Gene: 7920 ENSG00000204427 UniProt: O95870 OMIM: 142620

ABHD16A encodes a phosphatidylserine lipase that hydrolyzes phosphatidylserine to generate lysophosphatidylserine, a signaling lipid that regulates neurological processes. Mutations cause autosomal recessive spastic paraplegia 86, characterized by progressive spasticity primarily affecting the lower extremities. The gene shows high constraint against loss-of-function variants (LOEUF 0.384), suggesting intolerance to protein-disrupting changes.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.381 OMIM phenotype

Clinical Summary— ABHD16A

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.22) despite low pLI — interpret in context.

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ClinVar Variants

8 unique Pathogenic / Likely Pathogenic· 69 VUS of 117 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.38LOEUF

pLI 0.473

Z-score 4.63

OE 0.22 (0.13–0.38)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

2.48Z-score

OE missense 0.62 (0.55–0.69)

207 obs / 334.6 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.22 (0.13–0.38)

0≤0.351.4

Missense OE?0.62 (0.55–0.69)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 9 / 40.9Missense obs/exp: 207 / 334.6Syn Z: 1.02

ClinVar Variant Classifications

117 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5

Likely Pathogenic3

VUS69

Likely Benign13

Benign1

Conflicting2

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	4	1	0	0	5
Likely Pathogenic	3	0	0	0	3
VUS	2	66	1	0	69
Likely Benign	0	9	1	3	13
Benign	0	0	0	1	1
Conflicting	—				2
Total	9	76	2	4	93

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

9 pathogenic / likely-pathogenic (of 13) ClinVar copy-number / structural variants overlap ABHD16A — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →