PRR30

Summary

PRR30 (proline rich 30, HGNC:28677) is a protein-coding gene on chromosome 2p23.3, encoding Proline-rich protein 30 (Q53SZ7).

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_178553

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28677
Approved symbol	PRR30
Name	proline rich 30
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC44505
Ensembl gene	ENSG00000186143
Ensembl biotype	protein_coding
Entrez	339779

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000335524, ENST00000432962

RefSeq mRNA: 1 — MANE Select: NM_178553 NM_178553

CCDS: CCDS1739

Canonical transcript exons

ENST00000335524 — 3 exons

Exon	Start	End
ENSE00001335855	27138970	27139022
ENSE00001335856	27136848	27138694
ENSE00001335858	27139303	27139410

Expression profiles

Bgee: expression breadth broad, 33 present calls, max score 96.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1851 / max 180.8851, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
27453	0.1222	3
27454	0.0410	3
27455	0.0219	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.59	gold quality
right testis	UBERON:0004534	96.47	gold quality
testis	UBERON:0000473	93.03	gold quality
sperm	CL:0000019	91.97	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.29	gold quality
adult organism	UBERON:0007023	75.94	gold quality
secondary oocyte	CL:0000655	71.91	gold quality
buccal mucosa cell	CL:0002336	67.46	gold quality
mammary duct	UBERON:0001765	66.62	gold quality
epithelium of mammary gland	UBERON:0003244	66.55	gold quality
esophagus squamous epithelium	UBERON:0006920	61.15	gold quality
pancreatic ductal cell	CL:0002079	59.24	silver quality
palpebral conjunctiva	UBERON:0001812	59.02	gold quality
bronchial epithelial cell	CL:0002328	58.55	gold quality
oocyte	CL:0000023	58.37	gold quality
tendon of biceps brachii	UBERON:0008188	57.92	gold quality
bronchus	UBERON:0002185	57.71	gold quality
mucosa of paranasal sinus	UBERON:0005030	57.20	gold quality
nasal cavity epithelium	UBERON:0005384	57.10	gold quality
decidua	UBERON:0002450	56.58	gold quality
myocardium	UBERON:0002349	56.55	gold quality
endothelial cell	CL:0000115	55.72	gold quality
jejunal mucosa	UBERON:0000399	55.21	gold quality
epithelial cell of pancreas	CL:0000083	54.56	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
parotid gland	UBERON:0001831	54.07	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
oviduct epithelium	UBERON:0004804	53.23	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting PRR30, 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-6780A-5P	99.88	66.69	2776
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-4656	98.79	66.22	1306
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-499B-5P	98.35	68.39	988
HSA-MIR-92A-1-5P	98.28	64.51	631
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-6886-3P	96.96	66.36	844
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-6823-5P	96.26	65.69	919
HSA-MIR-3675-5P	95.90	65.80	474

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prr30	ENSMUSG00000042888
rattus_norvegicus	Prr30	ENSRNOG00000025726

Protein

Protein identifiers

Proline-rich protein 30 — Q53SZ7 (reviewed: Q53SZ7)

All UniProt accessions (2): C9JVA3, Q53SZ7

RefSeq proteins (1): NP_848648* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031461	DUF4679	Family

Pfam: PF15728

UniProt features (12 total): compositionally biased region 6, region of interest 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53SZ7-F1	59.04	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): GGTGTGT_MIR329, CAGCTG_AP4_Q5, HEB_Q6, MIR4728_5P, MIR6785_5P, MIR149_3P, MIR6883_5P, MIR6764_5P, MIR1915_3P, MIR1227_5P, chr2p23, MIR92A_1_5P, GSE2405_0H_VS_6H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_DN, GSE2405_HEAT_KILLED_VS_LIVE_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_24H_UP, GSE1566_WT_VS_EZH2_KO_LN_TCELL_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

264 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR30	FAM24A	A6NFZ4	574
PRR30	TEX38	Q6PEX7	520
PRR30	AXDND1	Q5T1B0	518
PRR30	IQCF6	A8MYZ5	506
PRR30	SPATA31F1	Q6ZU69	505
PRR30	CIMIP2A	Q6J272	474
PRR30	TRMT10B	Q6PF06	461
PRR30	ACTRT2	Q8TDY3	447
PRR30	CPXCR1	Q8N123	444
PRR30	RNF148	Q8N7C7	434
PRR30	LYZL6	O75951	430
PRR30	GARIN1B	Q96KD3	422
PRR30	NT5C1B	Q96P26	421
PRR30	TAFA3	Q7Z5A8	417
PRR30	LELP1	Q5T871	400

IntAct

12 interactions, top by confidence:

A	B	Type	Score
CYSRT1	PRR30	psi-mi:“MI:0915”(physical association)	0.560
PRR30	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-2	PRR30	psi-mi:“MI:0915”(physical association)	0.560
PRR30	IL1R2	psi-mi:“MI:0915”(physical association)	0.400
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
PRR30	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000
PRR30	KRTAP6-2	psi-mi:“MI:0915”(physical association)	0.000
PRR30	SPMIP9	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): PRR30 (Two-hybrid), KRTAP6-2 (Two-hybrid), CYSRT1 (Two-hybrid), PRR30 (Two-hybrid), PRR30 (Two-hybrid), IL1R2 (Affinity Capture-MS), PRR30 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTH6, A0A1B0GUW6, A0A1D5RMD1, A0A1W2PPK0, A2A9I7, A2AQH4, A6NCI8, A6NFR6, C4P6S0, O15027, O77645, O94993, O97939, P0C205, P0C206, P26632, P29258, Q0P670, Q0VAV2, Q2YDJ5, Q3V3Q4, Q4JK59, Q53SZ7, Q5BI31, Q5DTW7, Q5H9F3, Q5JRM2, Q5NCY0, Q5SSZ7, Q5VV67, Q68FV4, Q6AXV6, Q6AYN3, Q6NZN1, Q7TSG5, Q86X51, Q8C5U4, Q8CH19, Q8JIS6, Q8K4E0

Diamond homologs: Q4R8E6, Q53SZ7, Q9D9B7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	70
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

227 predictions. Top by Δscore:

Variant	Effect	Δscore
2:27138964:TCTTA:T	donor_loss	0.9600
2:27138965:CTTA:C	donor_loss	0.9600
2:27138966:TTA:T	donor_loss	0.9600
2:27138967:TACCA:T	donor_loss	0.9600
2:27138968:A:C	donor_loss	0.9600
2:27139020:GACC:G	acceptor_loss	0.9600
2:27139024:T:C	acceptor_loss	0.9600
2:27138968:A:AC	donor_gain	0.9500
2:27138969:C:CC	donor_gain	0.9500
2:27139023:C:CC	acceptor_gain	0.9500
2:27139316:G:C	donor_gain	0.9400
2:27138692:GACCT:G	acceptor_loss	0.9000
2:27138693:ACCT:A	acceptor_loss	0.9000
2:27139302:CCTT:C	donor_loss	0.9000
2:27139019:GGAC:G	acceptor_gain	0.8900
2:27139303:C:G	donor_loss	0.8800
2:27138695:C:CC	acceptor_gain	0.8400
2:27138963:CTCT:C	donor_loss	0.8400
2:27139020:GAC:G	acceptor_gain	0.8300
2:27139187:AAT:A	donor_gain	0.8300
2:27139021:AC:A	acceptor_gain	0.7800
2:27139022:CC:C	acceptor_gain	0.7800
2:27138691:GGAC:G	acceptor_gain	0.7600
2:27139018:AGGAC:A	acceptor_gain	0.7200
2:27138970:C:A	donor_loss	0.7100
2:27138836:C:CT	acceptor_gain	0.6900
2:27138837:A:T	acceptor_gain	0.6900
2:27138573:T:TA	donor_gain	0.6800
2:27138571:CTT:C	donor_gain	0.6700
2:27138692:GAC:G	acceptor_gain	0.6700

AlphaMissense

2608 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:27137436:G:C	F298L	0.994
2:27137436:G:T	F298L	0.994
2:27137438:A:G	F298L	0.994
2:27137499:G:C	F277L	0.989
2:27137499:G:T	F277L	0.989
2:27137501:A:G	F277L	0.989
2:27137584:T:C	Y249C	0.989
2:27137437:A:G	F298S	0.986
2:27137503:G:T	A276D	0.986
2:27137576:A:G	C252R	0.986
2:27137585:A:G	Y249H	0.984
2:27137578:A:T	I251K	0.983
2:27137574:G:C	C252W	0.982
2:27137647:A:G	L228P	0.981
2:27137650:T:A	D227V	0.981
2:27137431:A:T	L300H	0.979
2:27137543:A:G	C263R	0.978
2:27137567:A:G	C255R	0.977
2:27137584:T:G	Y249S	0.977
2:27137500:A:G	F277S	0.975
2:27137509:A:T	L274Q	0.974
2:27137650:T:C	D227G	0.973
2:27137575:C:T	C252Y	0.972
2:27137650:T:G	D227A	0.969
2:27137425:A:T	L302Q	0.967
2:27137585:A:C	Y249D	0.967
2:27137500:A:C	F277C	0.966
2:27137542:C:T	C263Y	0.966
2:27137565:G:C	C255W	0.966
2:27137659:A:T	I224N	0.966

dbSNP variants (sampled 300 via entrez): RS1001589852 (2:27141242 A>G), RS1002061733 (2:27140803 T>G), RS1002153219 (2:27138567 C>G), RS1002164526 (2:27138826 C>T), RS1002998057 (2:27139518 T>G), RS1003673679 (2:27138524 C>A,T), RS1004216557 (2:27139135 T>C), RS1005074429 (2:27140764 C>G,T), RS1005167877 (2:27141166 G>A), RS1006160857 (2:27139495 C>A,T), RS1006478668 (2:27139302 C>G,T), RS1007003594 (2:27140915 C>T), RS1007057418 (2:27141257 C>T), RS1007338780 (2:27139219 G>C), RS1007391255 (2:27139486 T>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

7 associations (top):

Study	Trait	p-value
GCST010697_14	Cortical surface area (min-P)	2.000000e-09
GCST010698_75	Subcortical volume (min-P)	2.000000e-13
GCST010699_41	Brain morphology (min-P)	2.000000e-08
GCST010700_38	Cortical thickness (MOSTest)	3.000000e-08
GCST010701_56	Cortical surface area (MOSTest)	4.000000e-16
GCST010702_20	Subcortical volume (MOSTest)	2.000000e-64
GCST010703_76	Brain morphology (MOSTest)	1.000000e-16

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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