ABRACL

Summary

ABRACL (ABRA C-terminal like, HGNC:21230) is a protein-coding gene on chromosome 6q24.1, encoding Costars family protein ABRACL (Q9P1F3).

Predicted to be involved in regulation of actin filament-based process.

Source: NCBI Gene 58527 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 29 total — 7 pathogenic
• MANE Select transcript: NM_021243

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21230
Approved symbol	ABRACL
Name	ABRA C-terminal like
Location	6q24.1
Locus type	gene with protein product
Status	Approved
Aliases	PRO2013, HSPC280, Costars
Ensembl gene	ENSG00000146386
Ensembl biotype	protein_coding
Entrez	58527

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 40 protein_coding

ENST00000367660, ENST00000461027, ENST00000858336, ENST00000858337, ENST00000858338, ENST00000858339, ENST00000858340, ENST00000858341, ENST00000858342, ENST00000858343, ENST00000858344, ENST00000858345, ENST00000858346, ENST00000858347, ENST00000858348, ENST00000858349, ENST00000858350, ENST00000935028, ENST00000935029, ENST00000935030, ENST00000935031, ENST00000935032, ENST00000935033, ENST00000935034, ENST00000935035, ENST00000935036, ENST00000935037, ENST00000935038, ENST00000935039, ENST00000935040, ENST00000935041, ENST00000935042, ENST00000935043, ENST00000935044, ENST00000935045, ENST00000935046, ENST00000935047, ENST00000935048, ENST00000935049, ENST00000935050

RefSeq mRNA: 1 — MANE Select: NM_021243 NM_021243

CCDS: CCDS43509

Canonical transcript exons

ENST00000367660 — 3 exons

Exon	Start	End
ENSE00000975621	139034155	139034221
ENSE00001125972	139042719	139043302
ENSE00001445288	139028745	139028875

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 98.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 84.0945 / max 1577.8227, expressed in 1795 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70129	53.9755	1789
70130	27.6725	1737
70132	1.3037	828
70128	0.4938	248
70131	0.4107	194
70127	0.1963	69
70126	0.0421	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.54	gold quality
leukocyte	CL:0000738	98.46	gold quality
mucosa of transverse colon	UBERON:0004991	98.36	gold quality
cortical plate	UBERON:0005343	98.01	gold quality
thymus	UBERON:0002370	97.72	gold quality
rectum	UBERON:0001052	97.53	gold quality
ileal mucosa	UBERON:0000331	97.36	gold quality
granulocyte	CL:0000094	97.25	gold quality
vermiform appendix	UBERON:0001154	97.19	gold quality
ganglionic eminence	UBERON:0004023	96.84	gold quality
spleen	UBERON:0002106	96.46	gold quality
colonic mucosa	UBERON:0000317	96.43	gold quality
lymph node	UBERON:0000029	96.20	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.15	gold quality
palpebral conjunctiva	UBERON:0001812	96.03	gold quality
bone marrow	UBERON:0002371	95.44	gold quality
islet of Langerhans	UBERON:0000006	95.34	gold quality
corpus epididymis	UBERON:0004359	95.33	gold quality
duodenum	UBERON:0002114	94.94	gold quality
epithelium of nasopharynx	UBERON:0001951	94.83	gold quality
jejunal mucosa	UBERON:0000399	94.72	gold quality
germinal epithelium of ovary	UBERON:0001304	94.58	gold quality
gall bladder	UBERON:0002110	94.10	gold quality
caecum	UBERON:0001153	94.03	gold quality
blood	UBERON:0000178	93.79	gold quality
esophagus mucosa	UBERON:0002469	93.68	gold quality
transverse colon	UBERON:0001157	93.37	gold quality
tonsil	UBERON:0002372	93.13	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.09	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.04	gold quality

Single-cell (SCXA)

Detected in 15 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-ENAD-21	yes	285.15
E-CURD-7	yes	225.09
E-HCAD-5	yes	64.59
E-GEOD-134144	yes	37.16
E-CURD-46	yes	23.51
E-HCAD-1	yes	18.05
E-GEOD-81608	yes	16.57
E-MTAB-8410	yes	12.97
E-MTAB-10042	yes	8.92
E-CURD-114	yes	7.29
E-CURD-89	no	587.20
E-MTAB-10485	no	558.95
E-CURD-55	no	377.27
E-MTAB-9388	no	10.97
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting ABRACL, 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-3163	100.00	77.23	8605
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-154-3P	99.50	70.05	831
HSA-MIR-487A-3P	99.50	69.95	840
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-520E-5P	99.27	68.90	1513

Literature-anchored findings (GeneRIF, showing 4)

• Solution structure of the human HSPC280 protein (PMID:21082705)
• Human Costars Family Protein ABRACL Modulates Actin Dynamics and Cell Migration and Associates with Tumorigenic Growth. (PMID:33670794)
• miR-145-5p Inhibits the Proliferation, Migration, and Invasion of Esophageal Carcinoma Cells by Targeting ABRACL. (PMID:33728339)
• Actin-binding Rho activating C-terminal like (ABRACL) transcriptionally regulated by MYB proto-oncogene like 2 (MYBL2) promotes the proliferation, invasion, migration and epithelial-mesenchymal transition of breast cancer cells. (PMID:35341461)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	abracl	ENSDARG00000042876
mus_musculus	Abracl	ENSMUSG00000078453
rattus_norvegicus	Abracl	ENSRNOG00000085760

Protein

Protein identifiers

Costars family protein ABRACL — Q9P1F3 (reviewed: Q9P1F3)

Alternative names: ABRA C-terminal-like protein

All UniProt accessions (2): Q9P1F3, Q5SZC9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the costars family.

RefSeq proteins (1): NP_067066* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027817	Costars_dom	Domain
IPR038095	Costars_sf	Homologous_superfamily
IPR044302	Costars	Family

Pfam: PF14705

UniProt features (9 total): helix 4, strand 3, chain 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2L2O	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P1F3-F1	94.81	0.90

Functional residue map

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

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN, GOLDRATH_ANTIGEN_RESPONSE, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, CAFFAREL_RESPONSE_TO_THC_24HR_5_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MILI_PSEUDOPODIA_CHEMOTAXIS_UP, LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP, VANTVEER_BREAST_CANCER_ESR1_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, YOSHIMURA_MAPK8_TARGETS_DN, KARLSSON_TGFB1_TARGETS_UP, GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN, PASINI_SUZ12_TARGETS_DN

GO Biological Process (1): regulation of actin filament-based process (GO:0032970)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
actin filament-based process	1
regulation of cellular process	1

Protein interactions and networks

STRING

618 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ABRACL	SMIM18	P0DKX4	555
ABRACL	TTC9B	Q8N6N2	504
ABRACL	IRGQ	Q8WZA9	494
ABRACL	DMAC2	Q9NW81	439
ABRACL	LRFN3	Q9BTN0	435
ABRACL	CXorf38	Q8TB03	430
ABRACL	MEF2C	Q06413	416
ABRACL	SBK1	Q52WX2	405
ABRACL	NBPF14	Q5TI25	399
ABRACL	TULP2	O00295	392
ABRACL	ABRA	Q8N0Z2	372
ABRACL	PKNOX2	Q96KN3	368
ABRACL	ZNF182	P17025	367
ABRACL	NALF1	B1AL88	363
ABRACL	NAA38	Q9BRA0	344
ABRACL	SORCS2	Q96PQ0	344

IntAct

6 interactions, top by confidence:

A	B	Type	Score
RPGRIP1L	ILVBL	psi-mi:“MI:2364”(proximity)	0.270
CNTRL	ANKRD28	psi-mi:“MI:2364”(proximity)	0.270
DCTN1	NACA	psi-mi:“MI:2364”(proximity)	0.270
SASS6	DVL2	psi-mi:“MI:2364”(proximity)	0.270
CNTRL	CCDC85C	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (11): ABRACL (Co-fractionation), ABRACL (Proximity Label-MS), ABRACL (Proximity Label-MS), ABRACL (Proximity Label-MS), ABRACL (Proximity Label-MS), ABRACL (Synthetic Lethality), ABRACL (Affinity Capture-RNA), ABRACL (Positive Genetic), ABRACL (Affinity Capture-MS), ABRACL (Proximity Label-MS), ABRACL (Affinity Capture-RNA)

ESM2 similar proteins: A0JN39, A2XKU9, A4FUD3, A4IHJ3, A7RHL5, A9NK39, B4YYA9, B5X8A5, D2SW95, O00232, O08810, O80526, P23514, P53618, Q01587, Q15029, Q28EN2, Q28EX9, Q2KJ25, Q2KJD7, Q32LQ4, Q3ZBN0, Q42450, Q498C5, Q4KML4, Q5F3X4, Q5FWT7, Q5M8Z0, Q5R4C4, Q5R6E0, Q5R922, Q5RAK7, Q5RBI3, Q5RJU0, Q5XGM3, Q5ZIA5, Q5ZJJ8, Q641F1, Q66HV4, Q6AVK1

Diamond homologs: A2XKU9, A4IHJ3, A7RHL5, A9NK39, B4YYA9, B5SNZ6, B5X8A5, Q3ZBN0, Q498C5, Q4KML4, Q558Y7, Q6AVK1, Q6TGV7, Q6V289, Q8BUZ1, Q8K4K7, Q8LBN7, Q8N0Z2, Q9P1F3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	7
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
147665	GRCh38/hg38 6q23.3-25.3(chr6:135358150-155455117)x3	Pathogenic
1684644	Single allele	Pathogenic
3062902	GRCh37/hg19 6q22.31-25.3(chr6:119840686-156623091)x3	Pathogenic
3062934	GRCh37/hg19 6q23.2-24.2(chr6:131569837-145572239)x3	Pathogenic
441897	GRCh37/hg19 6q23.2-24.2(chr6:133077239-143761582)x1	Pathogenic
625705	GRCh37/hg19 6q23.3-24.3(chr6:135239633-146997510)	Pathogenic
814871	GRCh37/hg19 6q23.2-24.1(chr6:133817341-140038401)x1	Pathogenic

SpliceAI

693 predictions. Top by Δscore:

Variant	Effect	Δscore
6:139028873:GAGG:G	donor_loss	1.0000
6:139034151:CCA:C	acceptor_loss	1.0000
6:139034153:A:AG	acceptor_gain	1.0000
6:139034154:G:GG	acceptor_gain	1.0000
6:139034154:GGCA:G	acceptor_gain	1.0000
6:139034222:G:GG	donor_gain	1.0000
6:139042714:ACTAG:A	acceptor_loss	1.0000
6:139042715:CTAGA:C	acceptor_loss	1.0000
6:139042716:TA:T	acceptor_loss	1.0000
6:139042717:A:AG	acceptor_gain	1.0000
6:139042717:A:AT	acceptor_loss	1.0000
6:139042718:G:GG	acceptor_gain	1.0000
6:139028871:GAGAG:G	donor_gain	0.9900
6:139028873:GAG:G	donor_gain	0.9900
6:139028876:GTGC:G	donor_gain	0.9900
6:139033426:G:GT	donor_gain	0.9900
6:139034154:GGC:G	acceptor_gain	0.9900
6:139034218:AAAA:A	donor_gain	0.9900
6:139034219:AAA:A	donor_gain	0.9900
6:139034219:AAAGT:A	donor_loss	0.9900
6:139034220:AA:A	donor_gain	0.9900
6:139034220:AAG:A	donor_loss	0.9900
6:139034221:AGTA:A	donor_loss	0.9900
6:139034224:AAG:A	donor_loss	0.9900
6:139042712:A:AG	acceptor_gain	0.9900
6:139042718:GAT:G	acceptor_gain	0.9900
6:139033427:A:T	donor_gain	0.9800
6:139034222:GT:G	donor_gain	0.9800
6:139034223:T:A	donor_gain	0.9800
6:139042717:AGAT:A	acceptor_gain	0.9800

AlphaMissense

525 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:139042745:T:C	F30L	0.998
6:139042747:T:A	F30L	0.998
6:139042747:T:G	F30L	0.998
6:139042799:G:A	G48R	0.998
6:139042799:G:C	G48R	0.998
6:139042800:G:A	G48E	0.998
6:139042806:T:A	L50H	0.998
6:139042806:T:C	L50P	0.998
6:139042815:C:A	A53E	0.997
6:139034189:T:C	L10S	0.996
6:139042814:G:C	A53P	0.996
6:139042755:T:A	L33H	0.995
6:139042810:A:C	K51N	0.995
6:139042810:A:T	K51N	0.995
6:139042812:C:A	A52D	0.995
6:139042857:T:C	L67P	0.995
6:139042791:C:A	A45E	0.994
6:139042755:T:G	L33R	0.993
6:139042788:A:T	E44V	0.993
6:139042806:T:G	L50R	0.993
6:139042811:G:C	A52P	0.993
6:139042833:T:A	V59E	0.993
6:139042854:T:A	L66H	0.993
6:139042854:T:C	L66P	0.993
6:139042789:A:C	E44D	0.992
6:139042789:A:T	E44D	0.992
6:139042790:G:C	A45P	0.992
6:139042808:A:G	K51E	0.992
6:139042819:A:C	K54N	0.992
6:139042819:A:T	K54N	0.992

dbSNP variants (sampled 300 via entrez): RS1000303029 (6:139036428 A>C,T), RS1000440422 (6:139036142 T>C,G), RS1000569400 (6:139029386 G>A), RS1000640733 (6:139037626 C>T), RS1000676420 (6:139035466 A>G), RS1000712576 (6:139042566 G>A), RS1000724489 (6:139030988 T>C), RS1000784006 (6:139029455 C>T), RS1001323711 (6:139031232 T>C), RS1001375627 (6:139043741 A>G), RS1001657328 (6:139030369 C>T), RS1001819611 (6:139031864 C>T), RS1001843523 (6:139043231 A>G), RS1001997408 (6:139037799 TAG>T), RS1002368974 (6:139036858 A>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:616744

GenCC curated gene-disease

Mondo (1): autoinflammatory syndrome, familial, Behcet-like (MONDO:0031384)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005956_33	Waist-to-hip ratio adjusted for BMI	6.000000e-09
GCST005962_46	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	6.000000e-08
GCST010204_156	Low density lipoprotein cholesterol levels	3.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression, decreases expression	6
sodium arsenite	decreases expression, increases expression	5
bisphenol A	decreases expression, decreases methylation, increases expression, affects cotreatment	4
Tetrachlorodibenzodioxin	increases expression	3
Cyclosporine	affects expression, increases expression	3
Aflatoxin B1	affects expression, decreases expression, increases expression	3
Air Pollutants	decreases expression, increases abundance	2
Smoke	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
tris(2-butoxyethyl) phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
cobaltous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
calfactant	decreases expression, affects cotreatment	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	decreases expression	1
Carbamazepine	affects expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Estradiol	decreases expression	1
Indomethacin	decreases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Ketoconazole	decreases expression	1
Plant Extracts	increases expression, affects cotreatment	1
Quercetin	affects expression	1
Rotenone	decreases expression	1

Clinical trials (associated diseases)

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