PABIR3

Summary

PABIR3 (PABIR family member 3, HGNC:25202) is a protein-coding gene on chromosome Xq26.3, encoding PABIR family member 1 (Q6P4D5).

Predicted to enable protein serine/threonine phosphatase inhibitor activity.

Source: NCBI Gene 159091 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 71 total
• MANE Select transcript: NM_001388447

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25202
Approved symbol	PABIR3
Name	PABIR family member 3
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	RP3-473B4.1
Ensembl gene	ENSG00000156500
Ensembl biotype	protein_coding
Entrez	159091

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 15 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000370784, ENST00000370785, ENST00000414371, ENST00000460216, ENST00000463842, ENST00000470657, ENST00000475361, ENST00000482240, ENST00000494709, ENST00000623326, ENST00000642481, ENST00000643150, ENST00000644752, ENST00000645176, ENST00000645256, ENST00000645288, ENST00000645433, ENST00000646004, ENST00000647516, ENST00000898787, ENST00000926068, ENST00000926069

RefSeq mRNA: 23 — MANE Select: NM_001388447 NM_001170779, NM_001170780, NM_001170781, NM_001170782, NM_001170783, NM_001170784, NM_001365743, NM_001365744, NM_001365745, NM_001365746, NM_001365747, NM_001365748, NM_001388440, NM_001388441, NM_001388442, NM_001388443, NM_001388444, NM_001388445, NM_001388446, NM_001388447, NM_001388448, NM_001388449, NM_138819

CCDS: CCDS14644, CCDS55500, CCDS55501, CCDS76028, CCDS87777, CCDS94669, CCDS94671, CCDS94672, CCDS94673, CCDS94674

Canonical transcript exons

ENST00000645433 — 11 exons

Exon	Start	End
ENSE00003494237	134845347	134845401
ENSE00003524754	134847383	134847475
ENSE00003541411	134814771	134814849
ENSE00003617763	134847883	134847971
ENSE00003623687	134807540	134807708
ENSE00003643283	134829226	134829282
ENSE00003719702	134845205	134845248
ENSE00003755928	134807237	134807341
ENSE00003818566	134852800	134852896
ENSE00003819991	134849167	134849228
ENSE00003916798	134854091	134854832

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 88.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1159 / max 106.7747, expressed in 1520 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197613	1.8178	815
197611	1.4269	666
197612	1.2220	666
197610	0.6916	184
197614	0.6103	278
197609	0.2644	118
209819	0.0642	31
197615	0.0187	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.46	gold quality
left ovary	UBERON:0002119	85.83	gold quality
bone marrow cell	CL:0002092	84.83	gold quality
adrenal tissue	UBERON:0018303	84.24	gold quality
ovary	UBERON:0000992	83.78	gold quality
right ovary	UBERON:0002118	82.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.80	gold quality
monocyte	CL:0000576	80.40	gold quality
leukocyte	CL:0000738	80.15	gold quality
right testis	UBERON:0004534	78.67	gold quality
left testis	UBERON:0004533	78.43	gold quality
testis	UBERON:0000473	78.35	gold quality
ventricular zone	UBERON:0003053	78.17	gold quality
ganglionic eminence	UBERON:0004023	77.34	gold quality
granulocyte	CL:0000094	77.23	gold quality
stromal cell of endometrium	CL:0002255	76.12	gold quality
sperm	CL:0000019	75.68	gold quality
smooth muscle tissue	UBERON:0001135	75.04	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	74.80	gold quality
lower esophagus muscularis layer	UBERON:0035833	74.76	gold quality
lower esophagus	UBERON:0013473	74.75	gold quality
left adrenal gland cortex	UBERON:0035825	74.44	gold quality
right adrenal gland cortex	UBERON:0035827	74.37	gold quality
adrenal gland	UBERON:0002369	74.00	gold quality
vermiform appendix	UBERON:0001154	73.95	gold quality
lower esophagus mucosa	UBERON:0035834	73.91	gold quality
germinal epithelium of ovary	UBERON:0001304	73.90	silver quality
right adrenal gland	UBERON:0001233	73.78	gold quality
body of uterus	UBERON:0009853	73.63	gold quality
spleen	UBERON:0002106	73.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting PABIR3, 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-6867-5P	100.00	82.21	3464
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-589-5P	98.72	66.96	927
HSA-MIR-4731-3P	98.56	68.60	1860

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pabir2	ENSDARG00000036500
mus_musculus	Pabir3	ENSMUSG00000036013
rattus_norvegicus	Pabir3	ENSRNOG00000028011
drosophila_melanogaster	CG4497	FBGN0031895
caenorhabditis_elegans		WBGENE00018518

Paralogs (2): PABIR2 (ENSG00000156504), PABIR1 (ENSG00000187866)

Protein

Protein identifiers

PABIR family member 1 — Q6P4D5 (reviewed: Q6P4D5)

All UniProt accessions (12): Q6P4D5, A0A087WU98, A0A2R8Y466, A0A2R8Y4Q6, A0A2R8Y5U9, A0A2R8Y6Q5, A0A2R8Y7I3, A0A2R8Y7S4, A0A2R8YFJ9, A0A2R8YFQ2, A0A2R8YGQ0, B3KQY3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the FAM122 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6P4D5-1	1	yes
Q6P4D5-2	2
Q6P4D5-3	3

RefSeq proteins (23): NP_001164250, NP_001164251, NP_001164252, NP_001164253, NP_001164254, NP_001164255, NP_001352672, NP_001352673, NP_001352674, NP_001352675, NP_001352676, NP_001352677, NP_001375369, NP_001375370, NP_001375371, NP_001375372, NP_001375373, NP_001375374, NP_001375375, NP_001375376, NP_001375377, NP_001375378, NP_620174 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026716	PBIR1/2/3	Family

UniProt features (5 total): splice variant 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P4D5-F1	63.45	0.15

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 117 (showing top): GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, TGACCTY_ERR1_Q2, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, OCT1_07, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_PROTEOLYSIS, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, GOBP_REGULATION_OF_PROTEOLYSIS, GOBP_PROTEIN_CATABOLIC_PROCESS, TGGAAA_NFAT_Q4_01, GOBP_PROTEOLYSIS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS

GO Biological Process (0):

GO Molecular Function (2): protein serine/threonine phosphatase inhibitor activity (GO:0004865), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein serine/threonine phosphatase activity	1
protein phosphatase inhibitor activity	1
binding	1

Protein interactions and networks

STRING

346 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PABIR3	SAGE1	Q9NXZ1	517
PABIR3	ADGRG2	Q8IZP9	507
PABIR3	CDK16	Q00536	491
PABIR3	SEPTIN6	Q14141	478
PABIR3	OR52M1	Q8NGK5	476
PABIR3	DIAPH2	O60879	465
PABIR3	STS	P08842	460
PABIR3	IL1RAPL1	Q9NZN1	458
PABIR3	SOWAHA	Q2M3V2	447
PABIR3	RIBC1	Q8N443	446
PABIR3	SFT2D1	Q8WV19	434
PABIR3	PBDC1	Q9BVG4	433
PABIR3	RNF157	Q96PX1	424
PABIR3	KIAA0513	O60268	419
PABIR3	TXNDC16	Q9P2K2	412

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CALR	PABIR3	psi-mi:“MI:0915”(physical association)	0.400
PABIR3	JCHAIN	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): FAM122C (Two-hybrid), FAM122C (Affinity Capture-RNA), FAM122C (Affinity Capture-RNA), IGHA1 (Affinity Capture-MS), DMBT1 (Affinity Capture-MS), IGJ (Affinity Capture-MS), PIGR (Affinity Capture-MS), MUC5B (Affinity Capture-MS), FAM122C (Affinity Capture-RNA)

ESM2 similar proteins: A0A182BSS5, A0A1P8B590, F4HXU3, F4IG60, F4J4Y5, F4JU69, O81791, O84275, P03124, P0C6G1, P0C6G2, P0DKG3, P0DO60, P43580, P48731, P50084, Q06924, Q0JXE7, Q3EAI1, Q4PSJ7, Q5PP38, Q5U1Z7, Q6AWW4, Q6IM80, Q6J1A5, Q6P4D5, Q6REU5, Q6ZUJ4, Q7Y219, Q84V03, Q86SG4, Q8H045, Q8K3A6, Q8LGS1, Q8W4H1, Q941I2, Q94CK6, Q9C9F4, Q9C9X6, Q9D9H3

Diamond homologs: Q5ZLN7, Q6AYT4, Q6NZE7, Q6P4D5, Q7Z309, Q96E09, Q9DB52

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1699 predictions. Top by Δscore:

Variant	Effect	Δscore
X:134814769:A:AG	acceptor_gain	1.0000
X:134814770:G:GG	acceptor_gain	1.0000
X:134814770:GTTTT:G	acceptor_gain	1.0000
X:134845199:TTACA:T	acceptor_loss	1.0000
X:134845200:TACAG:T	acceptor_loss	1.0000
X:134845202:CA:C	acceptor_loss	1.0000
X:134845203:A:AC	acceptor_loss	1.0000
X:134845244:GAATG:G	donor_gain	1.0000
X:134845247:TG:T	donor_gain	1.0000
X:134845247:TGG:T	donor_loss	1.0000
X:134845248:GG:G	donor_gain	1.0000
X:134845249:G:GG	donor_gain	1.0000
X:134845249:GTGA:G	donor_loss	1.0000
X:134845250:T:A	donor_loss	1.0000
X:134852894:GTA:G	donor_gain	1.0000
X:134854089:A:AG	acceptor_gain	1.0000
X:134854090:G:GG	acceptor_gain	1.0000
X:134807707:GG:G	donor_gain	0.9900
X:134807708:GG:G	donor_gain	0.9900
X:134807708:GGTGA:G	donor_loss	0.9900
X:134807709:G:GG	donor_gain	0.9900
X:134807709:GT:G	donor_loss	0.9900
X:134807710:TGA:T	donor_loss	0.9900
X:134807711:GAG:G	donor_loss	0.9900
X:134814770:GT:G	acceptor_gain	0.9900
X:134814770:GTT:G	acceptor_gain	0.9900
X:134814770:GTTT:G	acceptor_gain	0.9900
X:134814845:CTCTG:C	donor_loss	0.9900
X:134814846:TCTG:T	donor_loss	0.9900
X:134814847:CTGG:C	donor_loss	0.9900

AlphaMissense

1769 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:134829279:A:C	K81N	0.805
X:134829279:A:T	K81N	0.805
X:134845383:G:C	W109C	0.744
X:134845383:G:T	W109C	0.744
X:134807683:A:C	S29R	0.722
X:134807685:T:A	S29R	0.722
X:134807685:T:G	S29R	0.722
X:134814829:T:C	F57L	0.690
X:134814831:T:A	F57L	0.690
X:134814831:T:G	F57L	0.690
X:134852833:T:C	F127L	0.687
X:134852835:T:A	F127L	0.687
X:134852835:T:G	F127L	0.687
X:134814772:T:C	F38L	0.631
X:134814774:T:A	F38L	0.631
X:134814774:T:G	F38L	0.631
X:134829275:T:C	I80T	0.628
X:134829278:A:T	K81I	0.602
X:134829244:T:C	F70L	0.597
X:134829246:T:A	F70L	0.597
X:134829246:T:G	F70L	0.597
X:134852857:T:C	F135L	0.592
X:134852859:T:A	F135L	0.592
X:134852859:T:G	F135L	0.592
X:134854096:T:C	F150L	0.590
X:134854098:C:A	F150L	0.590
X:134854098:C:G	F150L	0.590
X:134845381:T:A	W109R	0.586
X:134845381:T:C	W109R	0.586

dbSNP variants (sampled 300 via entrez): RS1000029834 (X:134802095 T>C), RS1000180848 (X:134812673 G>A), RS1000255991 (X:134819817 G>A), RS1000290999 (X:134852251 G>C), RS1000339196 (X:134822609 C>T), RS1000471524 (X:134822035 A>G), RS1000557275 (X:134844499 A>C), RS1000586396 (X:134822862 G>A), RS1000694595 (X:134844144 C>G,T), RS1000720717 (X:134812085 T>A), RS1000841775 (X:134795986 G>A), RS1000898393 (X:134832607 G>T), RS1000902779 (X:134854710 G>A,C), RS1000916673 (X:134865221 G>A,T), RS1000928044 (X:134796848 G>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression	2
methylmercuric chloride	decreases expression	1
terbufos	decreases methylation	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
nickel sulfate	increases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
abrine	increases expression	1
NSC 689534	increases expression	1
Benzo(a)pyrene	affects methylation	1
Fonofos	decreases methylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Parathion	decreases methylation	1
Phthalic Acids	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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