PODNL1

Summary

PODNL1 (podocan like 1, HGNC:26275) is a protein-coding gene on chromosome 19p13.12, encoding Podocan-like protein 1 (Q6PEZ8).

An extracellular matrix structural constituent. Is active in collagen-containing extracellular matrix.

Source: NCBI Gene 79883 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 130 total
• MANE Select transcript: NM_001370095

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26275
Approved symbol	PODNL1
Name	podocan like 1
Location	19p13.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23447, SLRR5B
Ensembl gene	ENSG00000132000
Ensembl biotype	protein_coding
OMIM	621043
Entrez	79883

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 15 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000254320, ENST00000339560, ENST00000538371, ENST00000538517, ENST00000585607, ENST00000586075, ENST00000587288, ENST00000587458, ENST00000587954, ENST00000588317, ENST00000588764, ENST00000588872, ENST00000591353, ENST00000886044, ENST00000886045, ENST00000946318, ENST00000946319

RefSeq mRNA: 5 — MANE Select: NM_001370095 NM_001146254, NM_001146255, NM_001370095, NM_001411137, NM_024825

CCDS: CCDS12300, CCDS54225, CCDS54226, CCDS92538, CCDS92539

Canonical transcript exons

ENST00000588872 — 10 exons

Exon	Start	End
ENSE00000685302	13933878	13933993
ENSE00001385093	13935980	13936044
ENSE00001385724	13934254	13934410
ENSE00002770003	13931964	13932112
ENSE00002839746	13932798	13933455
ENSE00002900910	13931187	13931887
ENSE00003461762	13936367	13936460
ENSE00003486966	13937785	13938006
ENSE00003583907	13935721	13935830
ENSE00003816085	13938179	13938417

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 85.72.

FANTOM5 (CAGE): breadth broad, TPM avg 2.4287 / max 42.0770, expressed in 888 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179580	1.1186	470
179579	0.8107	340
179577	0.2517	125
179576	0.2476	135

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibial nerve	UBERON:0001323	85.72	gold quality
right coronary artery	UBERON:0001625	84.54	gold quality
apex of heart	UBERON:0002098	84.09	gold quality
lower esophagus mucosa	UBERON:0035834	83.17	gold quality
placenta	UBERON:0001987	83.13	gold quality
ascending aorta	UBERON:0001496	82.70	gold quality
thoracic aorta	UBERON:0001515	82.25	gold quality
left coronary artery	UBERON:0001626	81.65	gold quality
sural nerve	UBERON:0015488	80.33	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.09	gold quality
skin of leg	UBERON:0001511	79.99	gold quality
zone of skin	UBERON:0000014	79.58	gold quality
skin of abdomen	UBERON:0001416	79.27	gold quality
stromal cell of endometrium	CL:0002255	78.93	gold quality
descending thoracic aorta	UBERON:0002345	78.90	gold quality
mucosa of transverse colon	UBERON:0004991	78.67	gold quality
vagina	UBERON:0000996	78.06	gold quality
popliteal artery	UBERON:0002250	77.52	gold quality
tibial artery	UBERON:0007610	77.50	gold quality
esophagus mucosa	UBERON:0002469	77.07	gold quality
hypothalamus	UBERON:0001898	76.44	gold quality
cerebellar hemisphere	UBERON:0002245	73.39	gold quality
cerebellum	UBERON:0002037	73.29	gold quality
cerebellar cortex	UBERON:0002129	73.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	73.14	gold quality
substantia nigra	UBERON:0002038	72.15	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	72.08	gold quality
minor salivary gland	UBERON:0001830	71.33	gold quality
endocervix	UBERON:0000458	70.57	gold quality
adenohypophysis	UBERON:0002196	70.56	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-110499	no	8.81
E-ANND-3	no	2.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting PODNL1, 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-4425	100.00	67.59	1049
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-578	99.46	68.36	1787
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-4451	98.82	68.17	1455
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-7114-3P	98.42	66.53	569
HSA-MIR-3187-5P	98.36	65.74	1776
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-1285-3P	97.72	67.02	1932
HSA-MIR-5189-5P	97.72	66.96	1814
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-612	97.26	65.95	1597
HSA-MIR-6860	97.21	66.31	1656
HSA-MIR-4286	97.20	64.37	1587
HSA-MIR-4313	97.18	63.15	420
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-4486	96.96	60.61	931

Literature-anchored findings (GeneRIF, showing 1)

• PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. (PMID:34830454)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Podnl1	ENSMUSG00000012889
rattus_norvegicus	Podnl1	ENSRNOG00000006741

Paralogs (22): DCN (ENSG00000011465), RTN4R (ENSG00000040608), ASPN (ENSG00000106819), FLRT3 (ENSG00000125848), FLRT1 (ENSG00000126500), LRRC4 (ENSG00000128594), LRRC4B (ENSG00000131409), LRTM1 (ENSG00000144771), LRRC4C (ENSG00000148948), LRRTM1 (ENSG00000162951), LRRC15 (ENSG00000172061), PODN (ENSG00000174348), LRRTM4 (ENSG00000176204), BGN (ENSG00000182492), LRRC19 (ENSG00000184434), FLRT2 (ENSG00000185070), GP1BA (ENSG00000185245), RTN4RL1 (ENSG00000185924), RTN4RL2 (ENSG00000186907), NYX (ENSG00000188937), LRRC66 (ENSG00000188993), LRRTM3 (ENSG00000198739)

Protein

Protein identifiers

Podocan-like protein 1 — Q6PEZ8 (reviewed: Q6PEZ8)

All UniProt accessions (10): A0A2U3TZJ2, B7Z3M0, Q6PEZ8, K7EJ07, K7EMV0, K7EPI2, K7EPR1, K7ER84, K7ERE6, K7ESB1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Post-translational modifications. N-glycosylated.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class V subfamily.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6PEZ8-1	1	yes
Q6PEZ8-2	2
Q6PEZ8-3	3
Q6PEZ8-4	4

RefSeq proteins (5): NP_001139726, NP_001139727, NP_001357024, NP_001398066, NP_079101 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050333	SLRP	Family

Pfam: PF13855

UniProt features (28 total): repeat 17, splice variant 3, sequence conflict 3, signal peptide 1, chain 1, domain 1, glycosylation site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PEZ8-F1	87.24	0.82

Functional residue map

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

Glycosylation sites (1): 64

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, chr19p13, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, VDR_Q6, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, KRAS.AMP.LUNG_UP.V1_DN, KRAS.300_UP.V1_DN, KRAS.600_UP.V1_DN, GOCC_EXTERNAL_ENCAPSULATING_STRUCTURE, CDC5L_TARGET_GENES, GLI1_TARGET_GENES, ID1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): extracellular matrix structural constituent (GO:0005201), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular matrix (GO:0031012), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
structural molecule activity	1
extracellular matrix	1
binding	1
external encapsulating structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

658 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PODNL1	C19orf67	A6NJJ6	474
PODNL1	LGALS1	P09382	451
PODNL1	ADAMTS4	O75173	446
PODNL1	WRN	Q14191	407
PODNL1	PRKCG	P05129	406
PODNL1	FREM3	P0C091	356
PODNL1	NYX	Q9GZU5	354
PODNL1	C19orf53	Q9UNZ5	349
PODNL1	CTHRC1	Q96CG8	328
PODNL1	RHBG	Q9H310	327
PODNL1	DCAF4L1	Q3SXM0	325
PODNL1	LRR1	Q96L50	318
PODNL1	EPYC	Q99645	314
PODNL1	TMED8	Q6PL24	305
PODNL1	YJU2B	P13994	301

IntAct

8 interactions, top by confidence:

A	B	Type	Score
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
YWHAQ	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
BBS7	CDK4	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350
PCDH20	CAPN5	psi-mi:“MI:0914”(association)	0.350
PYCR3	ARHGAP32	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): PODNL1 (Affinity Capture-MS), PODNL1 (Affinity Capture-MS)

ESM2 similar proteins: A2VDH3, A6H793, B0BNK7, D2HFT7, D4ABX8, E9Q7T7, O75325, P22792, P40197, Q13641, Q149C3, Q1RMS4, Q2EEY0, Q2I0M4, Q3UVD5, Q3UY51, Q4KLL3, Q4R8Y9, Q50LG9, Q5I2M7, Q5I2M8, Q5PQV5, Q5VT99, Q6NUI6, Q6P3Y9, Q6PEZ8, Q6PJG9, Q6UY18, Q6ZSA7, Q7M6Z0, Q7TQ62, Q7Z5L7, Q80WD0, Q80WD1, Q80XU8, Q86UN2, Q86UN3, Q8BHA1, Q8BLY3, Q8K0S5

Diamond homologs: B1H134, B1H234, D3ZTV3, F1NUK7, G5EFX6, G5EG78, O43155, O88280, P19879, P20774, P24014, P58874, P79119, P83286, Q5R6T0, Q5RAC4, Q5RBL2, Q62000, Q6PEZ8, Q6RKD8, Q70AK3, Q810C1, Q8BGT1, Q8BLU0, Q8MJF1, Q96PX8, Q9DE65, Q9NR97, Q9NZU0, Q9NZU1, Q9UBM4, Q9W6H0, O02678, O46378, O46379, O46390, O46403, P21809, P21810, P22792

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	120
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1079 predictions. Top by Δscore:

Variant	Effect	Δscore
19:13933452:CTTG:C	acceptor_gain	1.0000
19:13933453:TTG:T	acceptor_gain	1.0000
19:13933454:TG:T	acceptor_gain	1.0000
19:13933456:C:CC	acceptor_gain	1.0000
19:13933456:C:CG	acceptor_loss	1.0000
19:13933457:T:A	acceptor_loss	1.0000
19:13933872:CTGTA:C	donor_loss	1.0000
19:13933873:TGTA:T	donor_loss	1.0000
19:13933875:TA:T	donor_loss	1.0000
19:13933876:A:AC	donor_gain	1.0000
19:13933876:A:C	donor_loss	1.0000
19:13933877:C:CC	donor_gain	1.0000
19:13933989:TTGTT:T	acceptor_gain	1.0000
19:13933990:TGTT:T	acceptor_gain	1.0000
19:13933991:GTT:G	acceptor_gain	1.0000
19:13933992:TT:T	acceptor_gain	1.0000
19:13933994:C:CC	acceptor_gain	1.0000
19:13933994:C:CG	acceptor_loss	1.0000
19:13933995:T:A	acceptor_loss	1.0000
19:13934241:A:AC	donor_gain	1.0000
19:13934242:C:CC	donor_gain	1.0000
19:13936363:TCA:T	donor_loss	1.0000
19:13936364:CACCT:C	donor_loss	1.0000
19:13936366:C:CT	donor_loss	1.0000
19:13937781:CCACC:C	donor_loss	1.0000
19:13937782:CACCT:C	donor_loss	1.0000
19:13937783:ACCTG:A	donor_loss	1.0000
19:13937784:C:CT	donor_loss	1.0000
19:13952640:TCA:T	donor_gain	1.0000
19:13952640:TCAAG:T	donor_loss	1.0000

AlphaMissense

3645 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000035776 (19:13931315 C>T), RS1000040102 (19:13941248 C>T), RS1000111425 (19:13954049 G>A), RS1000279383 (19:13942143 T>C,G), RS1000880519 (19:13949252 G>A), RS1000983558 (19:13942874 A>G), RS1001041808 (19:13954541 C>G,T), RS1001097555 (19:13949071 T>C,G), RS1001168382 (19:13943594 T>C), RS1001214925 (19:13940356 G>A), RS1001282199 (19:13946749 G>A), RS1001313566 (19:13946933 C>A), RS1001473587 (19:13953469 T>G), RS1001660093 (19:13953913 G>A), RS1001839602 (19:13953255 C>G,T)

Disease associations

OMIM: gene MIM:621043 | 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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	decreases expression, increases abundance	2
propionaldehyde	increases expression	1
deoxynivalenol	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
sodium arsenite	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
Dasatinib	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Camptothecin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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