PHGR1

Summary

PHGR1 (proline, histidine and glycine rich 1, HGNC:37226) is a protein-coding gene on chromosome 15q15.1, encoding Proline, histidine and glycine-rich protein 1 (C9JFL3).

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 24 total
• MANE Select transcript: NM_001145643

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37226
Approved symbol	PHGR1
Name	proline, histidine and glycine rich 1
Location	15q15.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000233041
Ensembl biotype	protein_coding
OMIM	621319
Entrez	644844

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000448599, ENST00000560745, ENST00000958414

RefSeq mRNA: 1 — MANE Select: NM_001145643 NM_001145643

CCDS: CCDS45225

Canonical transcript exons

ENST00000448599 — 4 exons

Exon	Start	End
ENSE00001594342	40353232	40353267
ENSE00001643116	40354345	40354352
ENSE00001689912	40351033	40351062
ENSE00001728960	40356073	40356434

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 99.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 7.2181 / max 2999.8095, expressed in 61 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146092	7.1999	60
146093	0.0182	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.97	gold quality
duodenum	UBERON:0002114	99.66	gold quality
rectum	UBERON:0001052	99.27	gold quality
small intestine	UBERON:0002108	98.25	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.25	gold quality
colonic epithelium	UBERON:0000397	97.15	gold quality
transverse colon	UBERON:0001157	96.90	gold quality
mucosa of stomach	UBERON:0001199	95.83	gold quality
vermiform appendix	UBERON:0001154	94.29	gold quality
intestine	UBERON:0000160	91.81	gold quality
colon	UBERON:0001155	89.72	gold quality
body of stomach	UBERON:0001161	87.62	gold quality
stomach	UBERON:0000945	84.38	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.23	silver quality
fundus of stomach	UBERON:0001160	77.70	gold quality
right coronary artery	UBERON:0001625	73.43	gold quality
right uterine tube	UBERON:0001302	68.12	gold quality
body of pancreas	UBERON:0001150	66.40	gold quality
smooth muscle tissue	UBERON:0001135	65.63	gold quality
ectocervix	UBERON:0012249	63.50	gold quality
thoracic mammary gland	UBERON:0005200	62.45	gold quality
prostate gland	UBERON:0002367	61.47	gold quality
lower esophagus mucosa	UBERON:0035834	60.35	gold quality
skin of leg	UBERON:0001511	59.13	gold quality
uterine cervix	UBERON:0000002	58.67	gold quality
right lobe of liver	UBERON:0001114	58.56	gold quality
right lung	UBERON:0002167	58.52	gold quality
left uterine tube	UBERON:0001303	57.76	gold quality
right ovary	UBERON:0002118	57.14	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-MTAB-8410	yes	31769.90
E-CURD-122	yes	30498.89
E-CURD-46	yes	27761.61
E-CURD-88	yes	27755.62
E-HCAD-11	yes	5441.28
E-MTAB-9906	yes	4501.76
E-MTAB-9543	yes	2772.22
E-ANND-5	yes	629.08
E-GEOD-125970	yes	78.29
E-CURD-114	yes	12.25
E-MTAB-5061	no	3.87
E-HCAD-31	no	3.66
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting PHGR1, 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-6077	99.99	68.04	2299
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-4695-5P	99.06	64.87	1151
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-581	98.39	67.42	835

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Proline, histidine and glycine-rich protein 1 — C9JFL3 (reviewed: C9JFL3)

All UniProt accessions (2): A0A1L2EC20, C9JFL3

RefSeq proteins (1): NP_001139115* (*=MANE)

Domains & families (InterPro)

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JFL3-F1	47.23	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): AKT_UP_MTOR_DN.V1_DN, GSE10094_LCMV_VS_LISTERIA_IND_EFF_CD4_TCELL_DN, MIR6077, MIR4687_3P, GSE17721_CTRL_VS_LPS_8H_BMDC_DN, GSE17721_CTRL_VS_CPG_4H_BMDC_DN, GSE17721_CTRL_VS_GARDIQUIMOD_2H_BMDC_UP, MURARO_PANCREAS_DELTA_CELL, MURARO_PANCREAS_EPSILON_CELL, BUSSLINGER_GASTRIC_IMMATURE_PIT_CELLS, BUSSLINGER_GASTRIC_MATURE_PIT_CELLS, BUSSLINGER_DUODENAL_MATURE_ENTEROCYTES, DESCARTES_FETAL_LUNG_NEUROENDOCRINE_CELLS, DESCARTES_FETAL_PANCREAS_ISLET_ENDOCRINE_CELLS, DESCARTES_FETAL_STOMACH_MUC13_DMBT1_POSITIVE_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

284 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHGR1	NALF1	B1AL88	544
PHGR1	OR5H1	A6NKK0	479
PHGR1	NEMP2	A6NFY4	475
PHGR1	GAGE12J	A6NER3	473
PHGR1	SPDYC	Q5MJ68	391
PHGR1	CCDC178	Q5BJE1	374
PHGR1	FAM184A	Q8NB25	358
PHGR1	RBM46	Q8TBY0	339
PHGR1	HAUS1	Q96CS2	324
PHGR1	CATSPER4	Q7RTX7	321
PHGR1	CALCB	P10092	320
PHGR1	SPRR3	Q9UBC9	311
PHGR1	PRB3	Q04118	308
PHGR1	CTAGE1	Q96RT6	306
PHGR1	DEFB123	Q8N688	305

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: C0HM81, C4NZN9, C9JFL3, O18740, O22612, O31510, O94426, P02674, P03211, P04474, P06649, P0C7K4, P0C7K5, P0C7K6, P0DX63, P11898, P12796, P13396, P17816, P19469, P19470, P21748, P21749, P21750, P27781, P37703, P37705, P50438, P50439, P86797, P86798, P86960, Q01157, Q07202, Q09134, Q09982, Q1HVF7, Q20689, Q25055, Q27270

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

325 predictions. Top by Δscore:

Variant	Effect	Δscore
15:40351058:CTCAG:C	donor_loss	0.9600
15:40351059:TCAG:T	donor_loss	0.9600
15:40351060:CAGG:C	donor_loss	0.9600
15:40351061:AGG:A	donor_loss	0.9600
15:40351062:GGT:G	donor_loss	0.9600
15:40351063:G:C	donor_loss	0.9600
15:40351064:T:A	donor_loss	0.9600
15:40356071:AGG:A	acceptor_gain	0.9300
15:40356072:GGG:G	acceptor_gain	0.9300
15:40356071:AG:A	acceptor_gain	0.9200
15:40356072:GG:G	acceptor_gain	0.9200
15:40356067:CCACA:C	acceptor_loss	0.8900
15:40356068:CACAG:C	acceptor_loss	0.8900
15:40356070:CAGG:C	acceptor_loss	0.8900
15:40356071:A:AG	acceptor_gain	0.8900
15:40356071:A:G	acceptor_loss	0.8900
15:40356072:G:GG	acceptor_gain	0.8900
15:40356060:T:A	acceptor_loss	0.8800
15:40356069:ACAGG:A	acceptor_gain	0.8800
15:40356072:GGGGC:G	acceptor_gain	0.8700
15:40354471:G:GT	donor_gain	0.8600
15:40356069:ACAG:A	acceptor_gain	0.8600
15:40356071:AGGG:A	acceptor_gain	0.8600
15:40356072:GGGG:G	acceptor_gain	0.8600
15:40354437:G:GT	donor_gain	0.8500
15:40356069:A:AG	acceptor_gain	0.7800
15:40351065:A:C	donor_gain	0.7500
15:40353079:G:GT	donor_gain	0.7300
15:40356058:T:G	acceptor_loss	0.7300
15:40354344:G:GC	acceptor_gain	0.7000

AlphaMissense

526 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:40353262:A:T	D2V	0.617
15:40354351:A:T	K6M	0.615
15:40356117:C:G	C21W	0.605
15:40356150:C:G	C32W	0.595
15:40354352:G:C	K6N	0.594
15:40354352:G:T	K6N	0.594
15:40356183:C:G	C43W	0.575
15:40356216:C:G	C54W	0.573

dbSNP variants (sampled 300 via entrez): RS1000839015 (15:40352692 C>T), RS1001397488 (15:40352911 T>C), RS1001959475 (15:40353904 G>A), RS1002599856 (15:40356408 C>T), RS1002669105 (15:40350016 C>T), RS1002825000 (15:40350220 G>A), RS1002869831 (15:40355030 G>A), RS1003672861 (15:40351034 G>A,C), RS1003948403 (15:40351539 G>A), RS1004275931 (15:40356452 T>C), RS1004721362 (15:40356045 C>G), RS1004843728 (15:40352527 C>T), RS1004922020 (15:40350597 G>C), RS1005361112 (15:40350369 T>C), RS1005845788 (15:40353750 C>G,T)

Disease associations

OMIM: gene MIM:621319 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST010725_23	Malaria	2.000000e-06
GCST010725_38	Malaria	3.000000e-06
GCST010725_80	Malaria	7.000000e-06
GCST90020025_442	Waist-to-hip ratio adjusted for BMI	2.000000e-10
GCST90020027_620	Waist-hip index	7.000000e-11
GCST90020029_282	Waist circumference adjusted for body mass index	9.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Calcitriol	increases expression, affects cotreatment	1
Rotenone	increases expression	1
Testosterone	affects cotreatment, increases expression	1
Tretinoin	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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