ABHD13

Summary

ABHD13 (abhydrolase domain containing 13, HGNC:20293) is a protein-coding gene on chromosome 13q33.3, encoding Protein ABHD13 (Q7L211).

Predicted to enable palmitoyl-(protein) hydrolase activity. Predicted to be involved in protein depalmitoylation. Located in membrane.

Source: NCBI Gene 84945 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 93 total — 38 pathogenic
• MANE Select transcript: NM_032859

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20293
Approved symbol	ABHD13
Name	abhydrolase domain containing 13
Location	13q33.3
Locus type	gene with protein product
Status	Approved
Aliases	bA153I24.2, FLJ14906, BEM46L1
Ensembl gene	ENSG00000139826
Ensembl biotype	protein_coding
OMIM	621039
Entrez	84945

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000375898, ENST00000857006, ENST00000857007, ENST00000857008, ENST00000925945, ENST00000925946, ENST00000949922

RefSeq mRNA: 1 — MANE Select: NM_032859 NM_032859

CCDS: CCDS32007

Canonical transcript exons

ENST00000375898 — 2 exons

Exon	Start	End
ENSE00001468760	108229199	108234243
ENSE00001468765	108218392	108218659

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 86.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.0644 / max 237.9970, expressed in 1806 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135970	11.2357	1781
135969	9.8286	1735

Top tissues by expression

244 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	86.98	gold quality
leukocyte	CL:0000738	86.70	gold quality
calcaneal tendon	UBERON:0003701	85.54	gold quality
islet of Langerhans	UBERON:0000006	83.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.46	gold quality
epithelial cell of pancreas	CL:0000083	80.76	silver quality
smooth muscle tissue	UBERON:0001135	80.29	gold quality
adrenal tissue	UBERON:0018303	79.98	gold quality
rectum	UBERON:0001052	79.95	gold quality
granulocyte	CL:0000094	79.57	gold quality
bone marrow	UBERON:0002371	78.96	gold quality
vermiform appendix	UBERON:0001154	78.48	gold quality
gall bladder	UBERON:0002110	78.06	gold quality
stromal cell of endometrium	CL:0002255	77.50	gold quality
cortical plate	UBERON:0005343	77.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.14	gold quality
pancreas	UBERON:0001264	77.08	gold quality
bone marrow cell	CL:0002092	76.87	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	76.84	gold quality
ganglionic eminence	UBERON:0004023	76.51	gold quality
pigmented layer of retina	UBERON:0001782	76.28	gold quality
right lung	UBERON:0002167	76.11	gold quality
descending thoracic aorta	UBERON:0002345	76.09	gold quality
ventricular zone	UBERON:0003053	76.09	gold quality
muscle of leg	UBERON:0001383	76.01	gold quality
gastrocnemius	UBERON:0001388	76.01	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.85	gold quality
thoracic aorta	UBERON:0001515	75.73	gold quality
lymph node	UBERON:0000029	75.69	gold quality
left coronary artery	UBERON:0001626	75.65	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

246 targeting ABHD13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-32-5P	99.98	75.21	1964

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	abhd13	ENSDARG00000059209
mus_musculus	Abhd13	ENSMUSG00000040396
rattus_norvegicus	Abhd13	ENSRNOG00000014598
drosophila_melanogaster	Bem46	FBGN0025109
caenorhabditis_elegans		WBGENE00008497
caenorhabditis_elegans		WBGENE00008498

Paralogs (7): ABHD12 (ENSG00000100997), ABHD17B (ENSG00000107362), ABHD17A (ENSG00000129968), ABHD12B (ENSG00000131969), ABHD17C (ENSG00000136379), ABHD16B (ENSG00000183260), ABHD16A (ENSG00000204427)

Protein

Protein identifiers

Protein ABHD13 — Q7L211 (reviewed: Q7L211)

Alternative names: Alpha/beta hydrolase domain-containing protein 13

All UniProt accessions (1): Q7L211

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the serine esterase family.

RefSeq proteins (1): NP_116248* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000073	AB_hydrolase_1	Domain
IPR029058	AB_hydrolase_fold	Homologous_superfamily

Pfam: PF00561

UniProt features (8 total): active site 3, sequence conflict 2, chain 1, transmembrane region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L211-F1	92.06	0.77

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 193 (charge relay system); 268 (charge relay system); 298 (charge relay system)

Glycosylation sites (1): 299

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 165 (showing top): TGCGCANK_UNKNOWN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, ATACCTC_MIR202, GOBP_MACROMOLECULE_DEACYLATION, GOCC_NEURON_PROJECTION, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOCC_CYTOPLASMIC_REGION, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_SOMATODENDRITIC_COMPARTMENT, GOCC_DENDRITE_CYTOPLASM, CAGCTTT_MIR320, NUYTTEN_NIPP1_TARGETS_DN, GOMF_THIOLESTER_HYDROLASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN

GO Biological Process (1): macromolecule depalmitoylation (GO:0098734)

GO Molecular Function (2): palmitoyl-(protein) hydrolase activity (GO:0008474), hydrolase activity (GO:0016787)

GO Cellular Component (3): membrane (GO:0016020), dendrite cytoplasm (GO:0032839), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
macromolecule deacylation	1
thiolester hydrolase activity	1
palmitoyl hydrolase activity	1
catalytic activity, acting on a protein	1
catalytic activity	1
dendrite	1
neuron projection cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

536 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABHD13	ABHD10	Q9NUJ1	601
ABHD13	ABHD16B	Q9H3Z7	600
ABHD13	ABHD16A	O95870	590
ABHD13	LYPLA2	O95372	589
ABHD13	LYPLA1	O75608	588
ABHD13	ABHD14A	Q9BUJ0	552
ABHD13	ABHD8	Q96I13	535
ABHD13	PAFAH2	Q99487	528
ABHD13	ABHD11	Q8NFV4	527
ABHD13	MFAP3	P55082	524
ABHD13	ABHD1	Q96SE0	519
ABHD13	ABHD15	Q6UXT9	508
ABHD13	ABHD3	Q8WU67	502
ABHD13	LYPLAL1	Q5VWZ2	487
ABHD13	ABHD2	P08910	464

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SLC19A2	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC1A1	SCD	psi-mi:“MI:0914”(association)	0.350
ABHD13		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): ABHD13 (Proximity Label-MS), ABHD13 (Proximity Label-MS), ABHD13 (Proximity Label-MS), ABHD13 (Proximity Label-MS), ABHD13 (Proximity Label-MS), ABHD13 (Proximity Label-MS), ABHD13 (Affinity Capture-MS), ABHD13 (Affinity Capture-MS), ABHD13 (Proximity Label-MS), ABHD13 (Affinity Capture-MS), ABHD13 (Affinity Capture-MS)

ESM2 similar proteins: A0A7H0DN16, A5PJJ7, B5BLW5, D5H0J3, G5EDL5, O16925, O17795, O22898, O57245, O60095, O74427, O74628, O74878, P28321, P32604, P42840, P54069, P78898, P93711, P96084, Q17704, Q1ZXQ4, Q3TUU5, Q3ZC52, Q4JK73, Q54DM9, Q54K57, Q54NU9, Q556J2, Q5JUR7, Q5M875, Q5UQ83, Q5ZJL8, Q6AYS8, Q6IRP4, Q6QA32, Q7L211, Q7Z5P4, Q80UX8, Q8NBQ5

Diamond homologs: P42840, P54069, Q08DW9, Q32LS6, Q4R766, Q5ZIN0, Q5ZJL8, Q6AYT7, Q6IRP4, Q7L211, Q80UX8, Q8N2K0, Q8RXP6, Q99LR1, P9WLC6, P9WLC7, Q08C93, Q21221, Q5ZJX1, A0A084R1K6, A5PKD9, B4F753, B5DFK7, P0CU85, P77538, Q2HJ19, Q5XIJ5, Q6DCC5, Q6DD70, Q6DEY3, Q6GL10, Q6PCB6, Q7Z5M8, Q7ZVZ7, Q8VCV1, Q8XA81, Q8Z4M8, Q8ZN39, Q96GS6, Q99JW1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

93 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	38
Likely pathogenic	0
Uncertain significance	49
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
148757	GRCh38/hg38 13q33.1-34(chr13:102883322-114340331)x1	Pathogenic
148962	GRCh38/hg38 13q32.1-33.3(chr13:97213871-109162916)x1	Pathogenic
151756	GRCh38/hg38 13q33.2-34(chr13:105861075-114342258)x1	Pathogenic
1527791	GRCh37/hg19 13q32.3-34(chr13:100258328-115107733)	Pathogenic
1527796	GRCh37/hg19 13q33.1-34(chr13:104545892-115107733)	Pathogenic
1527797	GRCh37/hg19 13q33.2-34(chr13:106056749-115107733)	Pathogenic
1527798	GRCh37/hg19 13q33.2-34(chr13:106450862-115107733)	Pathogenic
152824	GRCh38/hg38 13q33.1-34(chr13:101762788-114340285)x3	Pathogenic
152966	GRCh38/hg38 13q33.3-34(chr13:107708655-112101112)x1	Pathogenic
161056	GRCh38/hg38 13q33.3-34(chr13:107918132-114327173)x1	Pathogenic
1808473	GRCh37/hg19 13q32.3-34(chr13:100334135-110383902)x1	Pathogenic
1808983	GRCh37/hg19 13q32.1-34(chr13:97142120-115107733)x1	Pathogenic
1809298	GRCh37/hg19 13q32.3-34(chr13:99421603-115107733)x3	Pathogenic
2579202	GRCh38/hg38 13q33.3-34(chr13:106425676-114326445)x1	Pathogenic
2579261	GRCh38/hg38 13q32.2-34(chr13:98343655-110990677)x1	Pathogenic
3063276	GRCh37/hg19 13q33.3(chr13:107440465-109161884)x1	Pathogenic
3063287	GRCh37/hg19 13q33.2-34(chr13:106591678-115107733)x1	Pathogenic
3063291	GRCh37/hg19 13q33.2-34(chr13:105761074-115107733)x1	Pathogenic
3063300	GRCh37/hg19 13q33.1-34(chr13:103149209-115107733)x1	Pathogenic
3063307	GRCh37/hg19 13q33.1-34(chr13:102421732-115107733)x1	Pathogenic
3148881	GRCh37/hg19 13q32.2-33.3(chr13:98773859-109277603)x1	Pathogenic
3242333	GRCh37/hg19 13q32.3-34(chr13:99892724-115108414)x3	Pathogenic
33799	GRCh38/hg38 13q33.3-34(chr13:107918132-114327173)x1	Pathogenic
3902834	Single allele	Pathogenic
394870	GRCh37/hg19 13q33.2-33.3(chr13:105620486-108955885)x1	Pathogenic
4075927	GRCh37/hg19 13q33.2-34(chr13:106321647-115107733)x1	Pathogenic
4076087	GRCh37/hg19 13q33.1-34(chr13:102745885-115107733)x1	Pathogenic
442271	GRCh37/hg19 13q33.1-34(chr13:103170306-115107733)x1	Pathogenic
442938	GRCh37/hg19 13q32.1-34(chr13:96586481-115107733)x1	Pathogenic
564076	GRCh37/hg19 13q33.3-34(chr13:108567578-115107733)x3	Pathogenic

SpliceAI

286 predictions. Top by Δscore:

Variant	Effect	Δscore
13:108218658:GA:G	donor_gain	1.0000
13:108218660:G:GG	donor_gain	1.0000
13:108218658:GAGT:G	donor_loss	0.9900
13:108218659:AGTA:A	donor_loss	0.9900
13:108218660:G:A	donor_loss	0.9900
13:108218661:TAAG:T	donor_loss	0.9900
13:108218655:TCTGA:T	donor_gain	0.9800
13:108218657:TGA:T	donor_gain	0.9800
13:108218658:GAG:G	donor_gain	0.9800
13:108218662:AA:A	donor_loss	0.9800
13:108218656:CTGA:C	donor_gain	0.9700
13:108221453:GA:G	donor_gain	0.9700
13:108221455:G:GG	donor_gain	0.9700
13:108229197:A:AG	acceptor_gain	0.9700
13:108229198:G:GG	acceptor_gain	0.9700
13:108218664:G:GG	donor_gain	0.9600
13:108230217:T:G	donor_gain	0.9600
13:108218580:G:GT	donor_gain	0.9500
13:108218663:A:AG	donor_gain	0.9500
13:108229194:TCTA:T	acceptor_loss	0.9500
13:108229195:CTA:C	acceptor_loss	0.9500
13:108229196:TA:T	acceptor_loss	0.9500
13:108229197:AGG:A	acceptor_loss	0.9500
13:108218654:GTC:G	donor_gain	0.9400
13:108218655:TCT:T	donor_gain	0.9400
13:108221459:T:G	donor_gain	0.9300
13:108230221:A:AG	donor_gain	0.9300
13:108218652:GAGTC:G	donor_gain	0.9200
13:108219005:ATCTT:A	donor_gain	0.9200
13:108221435:G:GT	donor_gain	0.9200

AlphaMissense

2193 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:108229582:G:T	G122W	0.999
13:108229583:G:T	G122V	0.999
13:108229587:T:A	N123K	0.999
13:108229587:T:G	N123K	0.999
13:108229596:C:A	N126K	0.999
13:108229596:C:G	N126K	0.999
13:108229607:G:T	R130M	0.999
13:108229679:G:A	G154E	0.999
13:108229679:G:T	G154V	0.999
13:108229720:G:C	D168H	0.999
13:108229790:G:A	G191D	0.999
13:108229795:T:C	S193P	0.999
13:108229802:G:A	G195D	0.999
13:108229802:G:T	G195V	0.999
13:108229868:A:T	N217I	0.999
13:108229869:C:A	N217K	0.999
13:108229869:C:G	N217K	0.999
13:108229873:T:C	F219L	0.999
13:108229875:T:A	F219L	0.999
13:108229875:T:G	F219L	0.999
13:108230000:T:C	L261P	0.999
13:108230012:G:A	G265E	0.999
13:108230020:G:C	D268H	0.999
13:108230021:A:C	D268A	0.999
13:108230021:A:T	D268V	0.999
13:108230054:T:C	L279P	0.999
13:108230104:G:T	G296W	0.999
13:108230105:G:A	G296E	0.999
13:108230110:C:G	H298D	0.999
13:108230112:C:A	H298Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000260042 (13:108223305 C>G), RS1000345896 (13:108229106 A>G), RS1000504303 (13:108225623 G>C), RS1000618045 (13:108220061 C>T), RS1000619068 (13:108225890 A>G), RS1000737457 (13:108219067 C>T), RS1000754196 (13:108228060 A>G), RS1000801421 (13:108219646 C>G,T), RS1000844459 (13:108232467 C>A,T), RS1001560857 (13:108232948 T>C), RS1001683293 (13:108226034 G>A), RS1001694975 (13:108233342 T>C), RS1001852841 (13:108219713 C>G), RS1002197814 (13:108226416 A>G), RS1002528468 (13:108222554 C>G,T)

Disease associations

OMIM: gene MIM:621039 | disease phenotypes: MIM:619148, MIM:609637

GenCC curated gene-disease

Mondo (2): chromosome 13q33-q34 deletion syndrome (MONDO:0030896), holoprosencephaly 5 (MONDO:0012322)

Orphanet (1): Holoprosencephaly (Orphanet:2162)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST000253_9	Attention deficit hyperactivity disorder and conduct disorder	1.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566464	Holoprosencephaly 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	2
Valproic Acid	decreases expression, increases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
butyraldehyde	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Irinotecan	decreases expression	1
Doxorubicin	decreases expression	1
Folic Acid	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin M1	decreases expression	1
Antirheumatic Agents	decreases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1NM	HAP1 ABHD13 (-) 1	Cancer cell line	Male
CVCL_E1NN	HAP1 ABHD13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.