PAMR1

Summary

PAMR1 (peptidase domain containing associated with muscle regeneration 1, HGNC:24554) is a protein-coding gene on chromosome 11p13, encoding Inactive serine protease PAMR1 (Q6UXH9). May play a role in regeneration of skeletal muscle.

Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region.

Source: NCBI Gene 25891 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 112 total
• MANE Select transcript: NM_001001991

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24554
Approved symbol	PAMR1
Name	peptidase domain containing associated with muscle regeneration 1
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	RAMP, DKFZP586H2123
Ensembl gene	ENSG00000149090
Ensembl biotype	protein_coding
Entrez	25891

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000527605, ENST00000529303, ENST00000531219, ENST00000534803, ENST00000615849, ENST00000619888, ENST00000621476, ENST00000622144, ENST00000903468, ENST00000903469, ENST00000953162, ENST00000953163, ENST00000953164

RefSeq mRNA: 4 — MANE Select: NM_001001991 NM_001001991, NM_001282675, NM_001282676, NM_015430

CCDS: CCDS31460, CCDS60759, CCDS60760, CCDS7898

Canonical transcript exons

ENST00000619888 — 11 exons

Exon	Start	End
ENSE00000993325	35441481	35441693
ENSE00000993327	35435903	35436135
ENSE00000993329	35434512	35434804
ENSE00000993330	35439627	35439693
ENSE00003462107	35492045	35492173
ENSE00003524241	35470601	35470818
ENSE00003573418	35474630	35474744
ENSE00003582213	35494096	35494272
ENSE00003622854	35468001	35468108
ENSE00003899181	35431827	35432892
ENSE00003900883	35525513	35525616

Expression profiles

Bgee: expression breadth ubiquitous, 237 present calls, max score 99.19.

FANTOM5 (CAGE): breadth broad, TPM avg 12.2356 / max 299.2983, expressed in 874 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119377	11.0503	852
119378	0.8288	408
119379	0.3565	190

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	99.19	gold quality
stromal cell of endometrium	CL:0002255	99.12	gold quality
tibia	UBERON:0000979	97.49	gold quality
hair follicle	UBERON:0002073	96.25	gold quality
mammalian vulva	UBERON:0000997	95.23	gold quality
mucosa of urinary bladder	UBERON:0001259	94.14	silver quality
cartilage tissue	UBERON:0002418	93.70	gold quality
vena cava	UBERON:0004087	92.50	gold quality
placenta	UBERON:0001987	91.48	gold quality
urinary bladder	UBERON:0001255	90.61	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	89.82	gold quality
ventral tegmental area	UBERON:0002691	89.73	silver quality
vagina	UBERON:0000996	89.43	gold quality
inferior olivary complex	UBERON:0002127	89.01	gold quality
parietal pleura	UBERON:0002400	89.01	gold quality
medulla oblongata	UBERON:0001896	88.94	silver quality
uterine cervix	UBERON:0000002	88.85	gold quality
synovial joint	UBERON:0002217	88.83	gold quality
lateral globus pallidus	UBERON:0002476	88.59	silver quality
olfactory bulb	UBERON:0002264	88.54	silver quality
gall bladder	UBERON:0002110	88.52	gold quality
endocervix	UBERON:0000458	88.38	gold quality
myometrium	UBERON:0001296	88.36	gold quality
cardia of stomach	UBERON:0001162	88.34	silver quality
superior vestibular nucleus	UBERON:0007227	88.18	silver quality
body of uterus	UBERON:0009853	88.17	gold quality
urethra	UBERON:0000057	88.15	gold quality
epithelium of mammary gland	UBERON:0003244	88.12	gold quality
ectocervix	UBERON:0012249	87.99	gold quality
mammary duct	UBERON:0001765	87.98	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	345.90
E-MTAB-6701	yes	51.96
E-HCAD-25	yes	24.24
E-ANND-3	yes	15.58
E-MTAB-9388	yes	10.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting PAMR1, 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-511-3P	99.99	68.85	1467
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-3177-5P	99.65	70.38	1174
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-4318	99.38	66.94	1505
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-4646-3P	98.65	66.98	693
HSA-MIR-634	97.74	67.11	818
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-2114-3P	95.45	66.11	579
HSA-MIR-6823-3P	95.45	66.14	704
HSA-MIR-6816-3P	95.05	66.08	459
HSA-MIR-12115	94.19	66.37	738

Literature-anchored findings (GeneRIF, showing 2)

• RAMP may play a role in the regeneration of skeletal muscle, and its down-regulation could be involved in the progression of Duchenne muscular dystrophy (PMID:15111323)
• PAMR1 is a putative tumor suppressor which is frequently inactivated by promoter hypermethylation in breast cancer tissues. (PMID:25370079)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pamr1b	ENSDARG00000093480
danio_rerio	pamr1a	ENSDARG00000103184
mus_musculus	Pamr1	ENSMUSG00000027188
rattus_norvegicus	Pamr1	ENSRNOG00000005348

Paralogs (1): F2 (ENSG00000180210)

Protein

Protein identifiers

Inactive serine protease PAMR1 — Q6UXH9 (reviewed: Q6UXH9)

Alternative names: Peptidase domain-containing protein associated with muscle regeneration 1, Regeneration-associated muscle protease homolog

All UniProt accessions (4): Q6UXH9, A0A087WXE9, E9PMN5, E9PQ70

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in regeneration of skeletal muscle.

Subcellular location. Secreted.

Induction. Strongly down-regulated in muscle cell lines derived from biopsies of 5 Duchenne muscular dystrophy (DMD) patients compared to a normal muscle cell line.

Similarity. Belongs to the peptidase S1 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6UXH9-1	1	yes
Q6UXH9-2	2
Q6UXH9-3	3

RefSeq proteins (4): NP_001001991, NP_001269604, NP_001269605, NP_056245 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000436	Sushi_SCR_CCP_dom	Domain
IPR000742	EGF	Domain
IPR000859	CUB_dom	Domain
IPR001254	Trypsin_dom	Domain
IPR001314	Peptidase_S1A	Family
IPR001881	EGF-like_Ca-bd_dom	Domain
IPR009003	Peptidase_S1_PA	Homologous_superfamily
IPR035914	Sperma_CUB_dom_sf	Homologous_superfamily
IPR035976	Sushi/SCR/CCP_sf	Homologous_superfamily
IPR043504
IPR051659	Serine_Protease_S1-Domain	Family

Pfam: PF00008, PF00084, PF00089, PF00431

UniProt features (26 total): disulfide bond 11, domain 5, sequence conflict 4, splice variant 2, signal peptide 1, chain 1, sequence variant 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXH9-F1	77.31	0.38

Functional residue map

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

Disulfide bonds (11): 239–250, 244–260, 262–271, 280–329, 315–342, 414–442, 489–505, 630–649, 661–697, 128–150, 177–199

Glycosylation sites (1): 614

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): CHANDRAN_METASTASIS_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, LU_TUMOR_VASCULATURE_UP, RIGGI_EWING_SARCOMA_PROGENITOR_DN, HFH4_01, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, ARGGGTTAA_UNKNOWN, BROWNE_HCMV_INFECTION_24HR_DN, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, CUI_TCF21_TARGETS_2_UP, ATF_01, MODULE_47, TGGAAA_NFAT_Q4_01, LU_TUMOR_ENDOTHELIAL_MARKERS_UP

GO Biological Process (1): proteolysis (GO:0006508)

GO Molecular Function (2): calcium ion binding (GO:0005509), serine-type endopeptidase activity (GO:0004252)

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein metabolic process	1
metal ion binding	1
endopeptidase activity	1
serine-type peptidase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1098 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PAMR1	SLC1A2	P43004	729
PAMR1	TRAF6	Q9Y4K3	496
PAMR1	SCARA5	Q6ZMJ2	457
PAMR1	SMIM12	Q96EX1	455
PAMR1	RNF151	Q2KHN1	434
PAMR1	MINDY3	Q9H8M7	414
PAMR1	MNMIP1	A4FU49	412
PAMR1	PDLIM2	Q96JY6	409
PAMR1	ENDOU	P21128	406
PAMR1	TCAIM	Q8N3R3	403
PAMR1	SHISA4	Q96DD7	403
PAMR1	SNAPC3	Q92966	402
PAMR1	LRRC40	Q9H9A6	401
PAMR1	CLPTM1L	Q96KA5	395
PAMR1	MAGEH1	Q9H213	388

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SNX1	SNX2	psi-mi:“MI:0914”(association)	0.740
PAMR1	SUCLG2	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (3): SUCLG2 (Proximity Label-MS), PAMR1 (Affinity Capture-MS), PAMR1 (Proximity Label-MS)

ESM2 similar proteins: A0A1D5NSM8, A2AVA0, B1AUH1, B3DK56, D3ZHH1, E9Q6D8, G5E8Q8, O18016, O97827, P0C6B8, P13671, P21180, P28175, P35442, P35918, P61134, P61135, P86091, Q03350, Q05793, Q08E66, Q26422, Q29RU4, Q2QI47, Q4LDE5, Q5E9P5, Q5G872, Q5MD89, Q5RDI1, Q6DI48, Q6DIV5, Q6GP28, Q6NZL8, Q6UXH9, Q6YI48, Q7RTY8, Q7TQN3, Q80TS3, Q811M5, Q8BIK6

Diamond homologs: B3EX01, B8JI71, B8VIV4, C6KFA3, F1RWC3, O08628, O08859, O14786, O35276, O35375, O57382, O60462, O60494, O70244, O75074, O88204, P07898, P13497, P28824, P35443, P42662, P42664, P42674, P49744, P56677, P60882, P70412, P78504, P79795, P79953, P82279, P97333, P97607, P98065, P98066, P98069, P98072, P98074, Q06441, Q15113

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2146 predictions. Top by Δscore:

Variant	Effect	Δscore
11:35432890:AATC:A	acceptor_loss	1.0000
11:35432891:AT:A	acceptor_gain	1.0000
11:35432891:ATCTA:A	acceptor_loss	1.0000
11:35432892:TCTAC:T	acceptor_loss	1.0000
11:35432893:C:CC	acceptor_gain	1.0000
11:35432893:C:CG	acceptor_loss	1.0000
11:35432894:T:G	acceptor_loss	1.0000
11:35434506:TCTTA:T	donor_loss	1.0000
11:35434507:CTTAC:C	donor_loss	1.0000
11:35434508:TTA:T	donor_loss	1.0000
11:35434509:TA:T	donor_loss	1.0000
11:35434510:ACCTG:A	donor_loss	1.0000
11:35434511:C:CT	donor_loss	1.0000
11:35434801:CAGA:C	acceptor_gain	1.0000
11:35434805:C:CC	acceptor_gain	1.0000
11:35441476:GTTAC:G	donor_loss	1.0000
11:35441477:TTAC:T	donor_loss	1.0000
11:35441478:TA:T	donor_loss	1.0000
11:35441480:C:CG	donor_loss	1.0000
11:35441689:AAGGA:A	acceptor_gain	1.0000
11:35441690:AGGA:A	acceptor_gain	1.0000
11:35441691:GGA:G	acceptor_gain	1.0000
11:35441692:GA:G	acceptor_gain	1.0000
11:35441692:GAC:G	acceptor_loss	1.0000
11:35441693:ACT:A	acceptor_loss	1.0000
11:35441694:C:CC	acceptor_gain	1.0000
11:35468000:CG:C	donor_gain	1.0000
11:35468000:CGAT:C	donor_gain	1.0000
11:35468104:GCATG:G	acceptor_gain	1.0000
11:35468105:CATG:C	acceptor_gain	1.0000

AlphaMissense

4733 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:35474668:C:A	W152C	1.000
11:35474668:C:G	W152C	1.000
11:35494232:C:A	W38C	1.000
11:35494232:C:G	W38C	1.000
11:35435931:C:A	W435C	0.999
11:35435931:C:G	W435C	0.999
11:35435933:A:G	W435R	0.999
11:35435933:A:T	W435R	0.999
11:35441509:C:A	W335C	0.999
11:35441509:C:G	W335C	0.999
11:35470654:G:A	S220F	0.999
11:35470660:A:G	F218S	0.999
11:35470774:T:A	D180V	0.999
11:35474670:A:G	W152R	0.999
11:35474670:A:T	W152R	0.999
11:35474675:C:G	C150S	0.999
11:35474676:A:T	C150S	0.999
11:35441490:A:G	C342R	0.998
11:35441511:A:G	W335R	0.998
11:35441511:A:T	W335R	0.998
11:35470627:A:G	F229S	0.998
11:35470630:C:T	G228D	0.998
11:35470654:G:T	S220Y	0.998
11:35470655:A:G	S220P	0.998
11:35470660:A:C	F218C	0.998
11:35470717:C:G	C199S	0.998
11:35470717:C:T	C199Y	0.998
11:35470718:A:G	C199R	0.998
11:35470718:A:T	C199S	0.998
11:35470768:A:T	V182D	0.998

dbSNP variants (sampled 300 via entrez): RS1000017741 (11:35523795 C>A,T), RS1000025531 (11:35461341 G>C,T), RS1000056643 (11:35461729 G>A), RS1000094089 (11:35467483 A>G), RS1000103499 (11:35470610 C>G,T), RS1000151769 (11:35513519 C>A,T), RS1000173415 (11:35484187 T>C), RS1000194095 (11:35453076 T>C), RS1000195877 (11:35487133 G>A), RS1000206404 (11:35436381 T>C), RS1000257187 (11:35447086 T>A,C), RS1000266646 (11:35483918 G>A,C), RS1000272611 (11:35442664 T>C), RS1000294960 (11:35529357 G>A), RS1000367769 (11:35454287 C>T)

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

3 associations (top):

Study	Trait	p-value
GCST002104_12	Bronchopulmonary dysplasia	2.000000e-06
GCST002183_7	Relative hand skill in reading disability	9.000000e-06
GCST003264_234	Post bronchodilator FEV1/FVC ratio	4.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009902	handedness
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, decreases expression, affects expression	7
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, increases abundance, increases expression	3
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Arsenic	increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, increases methylation, increases mutagenesis	2
Dexamethasone	affects cotreatment, decreases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
bisphenol F	affects cotreatment, decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	increases expression	1
glycidyl methacrylate	decreases expression	1
sodium arsenate	increases abundance, increases expression	1
nickel sulfate	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
incobotulinumtoxinA	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Fulvestrant	increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Calcitriol	decreases expression	1
Cisplatin	affects expression	1
Cytarabine	decreases expression	1

Clinical trials (associated diseases)

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