S100PBP

Summary

S100PBP (S100P binding protein, HGNC:25768) is a protein-coding gene on chromosome 1p35.1, encoding S100P-binding protein (Q96BU1).

This gene encodes a protein that was originally identified by its interaction with S100 calcium-binding protein P. Expression of this protein has been reported to be associated with pancreatic ductal adenocarcinoma. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 64766 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 119 total — 1 likely-pathogenic
• MANE Select transcript: NM_022753

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25768
Approved symbol	S100PBP
Name	S100P binding protein
Location	1p35.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12903, S100PBPR
Ensembl gene	ENSG00000116497
Ensembl biotype	protein_coding
OMIM	611889
Entrez	64766

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 33 protein_coding, 7 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000356689, ENST00000373475, ENST00000373476, ENST00000474103, ENST00000475486, ENST00000477248, ENST00000482212, ENST00000524535, ENST00000525203, ENST00000526230, ENST00000527692, ENST00000529027, ENST00000530552, ENST00000530710, ENST00000531123, ENST00000531256, ENST00000873000, ENST00000873001, ENST00000873002, ENST00000873003, ENST00000873004, ENST00000873005, ENST00000873006, ENST00000873007, ENST00000873008, ENST00000918542, ENST00000918543, ENST00000918544, ENST00000918545, ENST00000918546, ENST00000918547, ENST00000918548, ENST00000918549, ENST00000918550, ENST00000918551, ENST00000918552, ENST00000918553, ENST00000918554, ENST00000918555, ENST00000967138, ENST00000967139

RefSeq mRNA: 2 — MANE Select: NM_022753 NM_001256121, NM_022753

CCDS: CCDS30666

Canonical transcript exons

ENST00000373475 — 7 exons

Exon	Start	End
ENSE00001431499	32825313	32825429
ENSE00001460656	32855924	32858875
ENSE00002159611	32817653	32817689
ENSE00003484711	32853079	32853166
ENSE00003510736	32827993	32828081
ENSE00003619142	32829964	32830067
ENSE00003679277	32826098	32826930

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 93.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.1461 / max 325.6449, expressed in 1786 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2025	4.5518	1533
2023	3.9973	1553
2024	1.8708	1110
2026	0.5756	156
2022	0.0797	31
2021	0.0711	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	93.69	gold quality
left testis	UBERON:0004533	93.02	gold quality
germinal epithelium of ovary	UBERON:0001304	92.89	gold quality
tibia	UBERON:0000979	92.83	gold quality
testis	UBERON:0000473	92.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.35	gold quality
ventricular zone	UBERON:0003053	91.70	gold quality
parietal pleura	UBERON:0002400	91.48	gold quality
sural nerve	UBERON:0015488	91.33	gold quality
adrenal tissue	UBERON:0018303	91.07	gold quality
cerebellar hemisphere	UBERON:0002245	90.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.60	gold quality
cerebellar cortex	UBERON:0002129	90.59	gold quality
right ovary	UBERON:0002118	90.50	gold quality
colonic epithelium	UBERON:0000397	90.48	gold quality
left ovary	UBERON:0002119	90.43	gold quality
calcaneal tendon	UBERON:0003701	90.43	gold quality
ovary	UBERON:0000992	90.33	gold quality
granulocyte	CL:0000094	90.07	gold quality
pleura	UBERON:0000977	89.82	gold quality
cerebellum	UBERON:0002037	89.42	gold quality
spleen	UBERON:0002106	89.34	gold quality
visceral pleura	UBERON:0002401	89.27	gold quality
endocervix	UBERON:0000458	89.26	gold quality
caudate nucleus	UBERON:0001873	88.97	gold quality
ganglionic eminence	UBERON:0004023	88.95	gold quality
mucosa of stomach	UBERON:0001199	88.85	gold quality
right uterine tube	UBERON:0001302	88.79	gold quality
tibial nerve	UBERON:0001323	88.76	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.76
E-ENAD-17	no	571.48
E-GEOD-124858	no	229.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

113 targeting S100PBP, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-8075	99.97	67.20	962

Literature-anchored findings (GeneRIF, showing 5)

• can be added to the genetic progression model for pancreatic ductal adenocarcinoma. (PMID:15632002)
• S100P is a sensitive and specific marker for the detection of pancreatic ductal adenocarcinoma on FNAB specimens on cell-block and smear preparations. (PMID:18089492)
• S100P-binding protein mediates adhesion through regulation of cathepsin Z in pancreatic cancer cells. (PMID:22330678)
• Low S100PBP expression is associated with cervical cancer. (PMID:25156441)
• S100PBP is regulated by mutated KRAS and plays a tumour suppressor role in pancreatic cancer. (PMID:37794133)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	S100pbp	ENSMUSG00000040928
rattus_norvegicus	S100pbp	ENSRNOG00000007099
rattus_norvegicus		ENSRNOG00000085905

Protein

Protein identifiers

S100P-binding protein — Q96BU1 (reviewed: Q96BU1)

Alternative names: S100P-binding protein Riken

All UniProt accessions (7): A0A0S2Z5M0, E9PIY5, E9PIZ7, E9PL86, E9PMK1, E9PSA0, Q96BU1

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with S100P.

Subcellular location. Nucleus.

Tissue specificity. Expressed in brain, spleen, and lung. Not detected in pancreas or liver. In pancreas, expressed predominantly in islet cells and to a lesser extent in acinar cells, but not expressed in ductal cells. Up-regulated in various pancreatic ductal adenocarcinomas and pancreatic intraepithelial neoplasias. Detected in pancreatic ductal adenocarcinoma cells (at protein level). Not detected in non-neoplastic ductal epithelium (at protein level).

Isoforms (2)

UniProt ID	Names	Canonical?
Q96BU1-1	1	yes
Q96BU1-2	2

RefSeq proteins (2): NP_001243050, NP_073590* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026097	S100PBP	Family

Pfam: PF15427

UniProt features (12 total): compositionally biased region 5, region of interest 3, chain 1, splice variant 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96BU1-F1	54.56	0.03

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): 187

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 205 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, CEBP_Q2, GCM_DDX11, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, DOUGLAS_BMI1_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, P53_DECAMER_Q2, YNGTTNNNATT_UNKNOWN, TGGAAA_NFAT_Q4_01, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, TAATTA_CHX10_01, GOCC_RIBONUCLEOPROTEIN_GRANULE, chr1p35

GO Biological Process (0):

GO Molecular Function (2): calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytosol (GO:0005829), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
calcium ion binding	1
protein binding	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cellular anatomical structure	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

710 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
S100PBP	S100P	P25815	982
S100PBP	ZG16B	Q96DA0	517
S100PBP	FAM89A	Q96GI7	479
S100PBP	TMEM25	Q86YD3	384
S100PBP	ABHD14A	Q9BUJ0	370
S100PBP	S100A3	P33764	363
S100PBP	KRABD5	Q7Z2F6	357
S100PBP	S100A16	Q96FQ6	355
S100PBP	TPRG1	Q6ZUI0	354
S100PBP	HECW2	Q9P2P5	349
S100PBP	CTSZ	Q9UBR2	348
S100PBP	UPB1	Q9UBR1	337
S100PBP	WDR6	Q9NNW5	336
S100PBP	AGER	Q15109	334
S100PBP	FAM86C1P	Q9NVL1	328
S100PBP	JMJD6	Q6NYC1	328

IntAct

7 interactions, top by confidence:

A	B	Type	Score
NUDT21	S100PBP	psi-mi:“MI:0915”(physical association)	0.560
PCED1B	S100PBP	psi-mi:“MI:0915”(physical association)	0.500
PCED1B	S100PBP	psi-mi:“MI:0914”(association)	0.500
PCED1A	HSPD1	psi-mi:“MI:0914”(association)	0.350
NUDT21	S100PBP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): S100PBP (Affinity Capture-MS), S100PBP (Affinity Capture-MS), S100PBP (Affinity Capture-RNA), NUDT21 (Two-hybrid), S100PBP (Affinity Capture-MS), S100PBP (Affinity Capture-MS), S100PBP (Proximity Label-MS), S100PBP (Proximity Label-MS), S100PBP (Proximity Label-MS), S100PBP (Proximity Label-MS), S100PBP (Proximity Label-MS), S100PBP (Proximity Label-MS), S100PBP (Affinity Capture-MS), S100PBP (Affinity Capture-RNA), S100PBP (Affinity Capture-RNA)

ESM2 similar proteins: A0A087WRU1, A0JNH1, A2RUB1, A6QNQ6, B0S6S9, B1WC58, D3Z987, D3ZJ47, E1BC15, O60673, P28358, P28359, P56716, P70347, Q0P5X5, Q0VAV2, Q0VBV7, Q15468, Q2M2Z5, Q3UXL4, Q3V089, Q49A88, Q569L8, Q5BQN8, Q5CZC0, Q5QGS0, Q5T1N1, Q5VWN6, Q60988, Q61493, Q62924, Q6ZP01, Q6ZU52, Q6ZVD7, Q80U59, Q80WQ8, Q86WS4, Q86YC2, Q8CB14, Q8IUR6

Diamond homologs: Q28DZ0, Q3MHH3, Q4V7J0, Q96BU1, Q9D5K4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	81
Likely benign	16
Benign	10

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1700207	NM_003680.4(YARS1):c.46C>T (p.Arg16Trp)	Likely pathogenic

SpliceAI

2209 predictions. Top by Δscore:

Variant	Effect	Δscore
1:32825430:G:GG	donor_gain	1.0000
1:32825435:G:GT	donor_gain	1.0000
1:32825443:T:G	donor_gain	1.0000
1:32826927:CAAA:C	donor_gain	1.0000
1:32827973:A:AG	acceptor_gain	1.0000
1:32827974:T:G	acceptor_gain	1.0000
1:32827986:A:AG	acceptor_gain	1.0000
1:32827987:A:AG	acceptor_gain	1.0000
1:32827988:A:AG	acceptor_gain	1.0000
1:32827989:A:G	acceptor_gain	1.0000
1:32827991:A:G	acceptor_gain	1.0000
1:32827992:GCA:G	acceptor_gain	1.0000
1:32828081:GGTAA:G	donor_loss	1.0000
1:32829946:T:A	acceptor_gain	1.0000
1:32829947:G:A	acceptor_gain	1.0000
1:32829951:T:TA	acceptor_gain	1.0000
1:32830064:CAAGG:C	donor_loss	1.0000
1:32830065:AAG:A	donor_loss	1.0000
1:32830066:AGGTA:A	donor_loss	1.0000
1:32830068:GT:G	donor_loss	1.0000
1:32830069:T:C	donor_loss	1.0000
1:32817293:T:A	donor_gain	0.9900
1:32817933:C:CA	donor_gain	0.9900
1:32826097:GAA:G	acceptor_gain	0.9900
1:32826097:GAAAT:G	acceptor_gain	0.9900
1:32826926:ACAAA:A	donor_gain	0.9900
1:32826928:AAA:A	donor_gain	0.9900
1:32826929:AA:A	donor_gain	0.9900
1:32826930:AGTA:A	donor_loss	0.9900
1:32826931:G:GG	donor_gain	0.9900

AlphaMissense

2682 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:32855973:T:A	W388R	0.997
1:32855973:T:C	W388R	0.997
1:32855975:G:C	W388C	0.996
1:32855975:G:T	W388C	0.996
1:32856006:T:C	F399L	0.994
1:32856008:C:A	F399L	0.994
1:32856008:C:G	F399L	0.994
1:32855974:G:C	W388S	0.989
1:32856007:T:C	F399S	0.984
1:32830029:T:A	V329D	0.980
1:32853157:T:C	L368P	0.977
1:32856007:T:G	F399C	0.973
1:32830020:T:C	L326P	0.970
1:32853146:T:A	H364Q	0.970
1:32853146:T:G	H364Q	0.970
1:32830009:G:C	K322N	0.968
1:32830009:G:T	K322N	0.968
1:32855961:A:C	S384R	0.967
1:32855963:T:A	S384R	0.967
1:32855963:T:G	S384R	0.967
1:32853160:C:T	T369I	0.966
1:32853166:G:C	R371P	0.964
1:32855973:T:G	W388G	0.964
1:32855974:G:T	W388L	0.961
1:32855977:T:A	V389D	0.960
1:32856006:T:G	F399V	0.960
1:32855987:C:A	N392K	0.959
1:32855987:C:G	N392K	0.959
1:32853145:A:G	H364R	0.955
1:32855927:C:A	N372K	0.954

dbSNP variants (sampled 300 via entrez): RS1000095190 (1:32851017 C>G), RS1000130236 (1:32844193 G>A), RS1000188721 (1:32838258 C>T), RS1000192713 (1:32842881 C>A,T), RS1000239527 (1:32838562 G>A,T), RS1000274444 (1:32844829 A>C), RS1000516923 (1:32845778 C>T), RS1000572665 (1:32839594 C>T), RS1000575227 (1:32839963 C>T), RS1000585591 (1:32844578 G>A), RS1000630467 (1:32814771 C>T), RS1000641413 (1:32856387 G>A,C), RS1000695476 (1:32820566 C>T), RS1000723367 (1:32833098 T>G), RS1000781829 (1:32833441 A>G)

Disease associations

OMIM: gene MIM:611889 | disease phenotypes: MIM:608323, MIM:616263

GenCC curated gene-disease

Mondo (2): Charcot-Marie-Tooth disease dominant intermediate C (MONDO:0012012), neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset (MONDO:0024189)

Orphanet (1): Autosomal dominant intermediate Charcot-Marie-Tooth disease type C (Orphanet:100045)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C564257	Charcot-Marie-Tooth Disease, Dominant Intermediate C (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, decreases expression, affects expression, decreases methylation, affects cotreatment	8
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
FR900359	increases phosphorylation	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects 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
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases expression	1
Calcitriol	increases expression	1
Demecolcine	decreases expression	1
Doxorubicin	decreases expression	1
Hydralazine	increases expression, affects cotreatment	1
Copper Sulfate	decreases expression	1
tert-Butylhydroperoxide	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_E2JP	HAP1 S100PBP (-) 2	Cancer cell line	Male
CVCL_XS39	HAP1 S100PBP (-) 1	Cancer cell line	Male

Clinical trials (associated diseases)

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