COL20A1

Summary

COL20A1 (collagen type XX alpha 1 chain, HGNC:14670) is a protein-coding gene on chromosome 20q13.33, encoding Collagen alpha-1(XX) chain (Q9P218). Probable collagen protein.

Predicted to be located in collagen-containing extracellular matrix; endoplasmic reticulum lumen; and extracellular region. Predicted to be part of collagen trimer.

Source: NCBI Gene 57642 — RefSeq curated summary.

At a glance

• Gene–disease (curated): hereditary palmoplantar keratoderma (Limited, GenCC)
• Clinical variants (ClinVar): 301 total — 1 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_020882

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14670
Approved symbol	COL20A1
Name	collagen type XX alpha 1 chain
Location	20q13.33
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1510
Ensembl gene	ENSG00000101203
Ensembl biotype	protein_coding
OMIM	619390
Entrez	57642

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000358894, ENST00000415763, ENST00000422202, ENST00000455906, ENST00000471582, ENST00000479501, ENST00000494913, ENST00000496810, ENST00000894509, ENST00000938907

RefSeq mRNA: 1 — MANE Select: NM_020882 NM_020882

CCDS: CCDS46628

Canonical transcript exons

ENST00000358894 — 36 exons

Exon	Start	End
ENSE00000663393	63312420	63312549
ENSE00000663399	63319058	63319200
ENSE00000663400	63319487	63319596
ENSE00000856569	63309758	63309915
ENSE00000856570	63315404	63315439
ENSE00001410478	63293186	63293275
ENSE00001563363	63328079	63328127
ENSE00003470528	63325441	63325494
ENSE00003474099	63326752	63326823
ENSE00003474637	63297910	63298020
ENSE00003480561	63320039	63320197
ENSE00003487082	63311394	63311539
ENSE00003488141	63321013	63321099
ENSE00003495329	63313743	63313891
ENSE00003495444	63307971	63308090
ENSE00003505924	63310381	63310510
ENSE00003521148	63322058	63322111
ENSE00003544146	63295098	63295189
ENSE00003552700	63316553	63316691
ENSE00003555782	63305417	63305560
ENSE00003564929	63307490	63307648
ENSE00003568716	63327952	63327987
ENSE00003574827	63314072	63314201
ENSE00003577918	63312792	63312934
ENSE00003588427	63311916	63312055
ENSE00003594118	63309333	63309497
ENSE00003595032	63311625	63311748
ENSE00003602530	63305881	63306039
ENSE00003602678	63326096	63326149
ENSE00003622430	63329585	63329661
ENSE00003634044	63308542	63308706
ENSE00003678876	63325668	63325721
ENSE00003690224	63320291	63320368
ENSE00003694095	63313117	63313249
ENSE00003786935	63328331	63328498
ENSE00003936648	63330720	63334806

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 87.70.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4232 / max 48.4954, expressed in 107 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
185806	0.4232	107

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	87.70	gold quality
left testis	UBERON:0004533	86.85	gold quality
anterior cingulate cortex	UBERON:0009835	86.41	gold quality
right frontal lobe	UBERON:0002810	85.57	gold quality
amygdala	UBERON:0001876	84.91	gold quality
pancreatic ductal cell	CL:0002079	83.79	silver quality
testis	UBERON:0000473	83.59	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.75	gold quality
endothelial cell	CL:0000115	82.05	silver quality
nucleus accumbens	UBERON:0001882	80.45	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.33	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	79.75	gold quality
substantia nigra	UBERON:0002038	79.01	gold quality
tibialis anterior	UBERON:0001385	78.64	silver quality
spinal cord	UBERON:0002240	78.50	gold quality
neocortex	UBERON:0001950	78.17	gold quality
putamen	UBERON:0001874	78.09	gold quality
temporal lobe	UBERON:0001871	77.98	gold quality
Ammon’s horn	UBERON:0001954	77.88	gold quality
cerebral cortex	UBERON:0000956	77.74	gold quality
right hemisphere of cerebellum	UBERON:0014890	77.56	gold quality
midbrain	UBERON:0001891	77.50	gold quality
frontal cortex	UBERON:0001870	77.48	gold quality
hypothalamus	UBERON:0001898	77.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.84	gold quality
buccal mucosa cell	CL:0002336	76.81	gold quality
forebrain	UBERON:0001890	76.65	gold quality
brain	UBERON:0000955	76.28	gold quality
cerebellar hemisphere	UBERON:0002245	75.68	gold quality
cerebellar cortex	UBERON:0002129	75.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	5.58
E-ANND-3	yes	3.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting COL20A1, 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-6892-3P	99.68	66.40	1178
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-548V	99.29	69.47	1157
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-193B-5P	97.91	65.88	837

Literature-anchored findings (GeneRIF, showing 2)

• Our study proposes COL20A1 gene as another potential candidate gene for striate palmoplantar keratoderma (PPKS)which expand the spectrum of collagen proteins in the pathogenicity of Palmoplantar keratoderma. (PMID:29934816)
• Type XX Collagen Is Elevated in Circulation of Patients with Solid Tumors. (PMID:35456962)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Col20a1	ENSMUSG00000016356

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL16A1 (ENSG00000084636), COL9A3 (ENSG00000092758), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), COL6A2 (ENSG00000142173), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), EMID1 (ENSG00000186998), COL4A1 (ENSG00000187498), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-1(XX) chain — Q9P218 (reviewed: Q9P218)

All UniProt accessions (3): Q9P218, B7ZBI4, B7ZBI5

UniProt curated annotations — full annotation on UniProt →

Function. Probable collagen protein.

Subcellular location. Secreted. Extracellular space.

Tissue specificity. High expression in heart, lung, liver, skeletal muscle, kidney, pancreas, spleen, testis, ovary, subthalamic nucleus and fetal liver. Weak expression in other tissues tested.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9P218-1	1	yes
Q9P218-2	2
Q9P218-3	3

RefSeq proteins (1): NP_065933* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002035	VWF_A	Domain
IPR003961	FN3_dom	Domain
IPR008160	Collagen	Repeat
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036465	vWFA_dom_sf	Homologous_superfamily
IPR048287	TSPN-like_N	Domain
IPR050991	ECM_Regulatory_Proteins	Family

Pfam: PF00041, PF00092, PF01391

UniProt features (57 total): strand 27, domain 10, sequence conflict 5, compositionally biased region 4, region of interest 3, splice variant 3, signal peptide 1, chain 1, glycosylation site 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
5KF4	X-RAY DIFFRACTION	2.5
2DKM	SOLUTION NMR
2EE3	SOLUTION NMR
2EKJ	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P218-F1	73.88	0.24

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): 607

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1650814	Collagen biosynthesis and modifying enzymes
R-HSA-8948216	Collagen chain trimerization

MSigDB gene sets: 59 (showing top): GOCC_COLLAGEN_TRIMER, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, DARWICHE_PAPILLOMA_PROGRESSION_RISK, COATES_MACROPHAGE_M1_VS_M2_DN, MODULE_48, MODULE_95, GOCC_ENDOPLASMIC_RETICULUM_LUMEN, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, MARTENS_TRETINOIN_RESPONSE_UP, CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, MODULE_163

GO Biological Process (0):

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

GO Cellular Component (4): extracellular region (GO:0005576), collagen trimer (GO:0005581), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Collagen formation	1
Collagen biosynthesis and modifying enzymes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1
protein-containing complex	1
endoplasmic reticulum	1
intracellular organelle lumen	1
external encapsulating structure	1

Protein interactions and networks

STRING

930 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
COL20A1	CNIH1	O95406	495
COL20A1	CNIH3	Q8TBE1	490
COL20A1	ARSJ	Q5FYB0	448
COL20A1	PALMD	Q9NP74	439
COL20A1	RIC3	Q7Z5B4	429
COL20A1	IFT38	Q96AJ1	427
COL20A1	KLHL31	Q9H511	427
COL20A1	SEC16B	Q96JE7	423
COL20A1	ACAD10	Q6JQN1	418
COL20A1	TDRD7	Q8NHU6	405
COL20A1	UBE2H	P37286	400
COL20A1	MKNK1	Q9BUB5	385
COL20A1	AUTS2	Q8WXX7	383
COL20A1	COL26A1	Q96A83	382
COL20A1	ADAMTS14	Q8WXS8	350

IntAct

14 interactions, top by confidence:

A	B	Type	Score
GPC3	CLGN	psi-mi:“MI:0914”(association)	0.530
ATP5MC3	ATP5F1B	psi-mi:“MI:0914”(association)	0.530
JPT1	COL20A1	psi-mi:“MI:0915”(physical association)	0.400
UBE2B	COL20A1	psi-mi:“MI:0915”(physical association)	0.400
USP47	COL20A1	psi-mi:“MI:0915”(physical association)	0.400
COL20A1	FAM9B	psi-mi:“MI:0915”(physical association)	0.370
ECE1	COL20A1	psi-mi:“MI:0915”(physical association)	0.370
TEX11	COL20A1	psi-mi:“MI:0915”(physical association)	0.370
COL20A1	MANBA	psi-mi:“MI:0914”(association)	0.350
NUDT16	BCKDK	psi-mi:“MI:0914”(association)	0.350
COL20A1	TSC2	psi-mi:“MI:0914”(association)	0.350
CPLX3	ATE1	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (31): COL20A1 (Two-hybrid), COL20A1 (Two-hybrid), FAM9B (Two-hybrid), COL20A1 (Two-hybrid), GGACT (Affinity Capture-MS), TSC2 (Affinity Capture-MS), COL14A1 (Affinity Capture-MS), COL20A1 (Affinity Capture-MS), MEIS1 (Affinity Capture-MS), CDKN2C (Affinity Capture-MS), PBX2 (Affinity Capture-MS), GLS (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), COL20A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LHF2, A0JPB1, A2AJ76, A7LCJ3, A8E0Y8, E7FF10, O00241, O60500, P01874, P03988, P04221, P0DOX2, P0DOX3, P0DOX4, P0DOX6, P0DP72, P32507, P35590, P43121, P50895, Q06805, Q06806, Q148M6, Q15109, Q5TFQ8, Q5U5A3, Q5XI43, Q62230, Q62786, Q8HW98, Q8NDA2, Q8R2Y2, Q92154, Q923P0, Q93033, Q95KI3, Q96MS0, Q9BRK3, Q9BZZ2, Q9DBV4

Diamond homologs: A0A1D5NSM8, A0JNA2, A2AVA0, A2AX52, D3YXF5, O02839, O19063, O35764, O43405, O70340, O76536, O89029, O95502, O96530, P02741, P02743, P06205, P06206, P06207, P06681, P07202, P07629, P08607, P09871, P0C6B8, P10643, P12246, P13944, P14151, P14847, P15697, P18337, P23680, P32018, P47970, P47971, P47972, P48199, P49254, P49262

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	259
Likely benign	28
Benign	2

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
564629	GRCh37/hg19 20q13.33(chr20:61815143-62318983)x1	Pathogenic
1326328	GRCh37/hg19 20q13.33(chr20:61944468-62104030)	Likely pathogenic

SpliceAI

7330 predictions. Top by Δscore:

Variant	Effect	Δscore
20:63294752:G:GT	donor_gain	1.0000
20:63297908:A:AG	acceptor_gain	1.0000
20:63297909:G:GG	acceptor_gain	1.0000
20:63297909:GCA:G	acceptor_gain	1.0000
20:63297909:GCAA:G	acceptor_gain	1.0000
20:63305553:GTTT:G	donor_gain	1.0000
20:63305557:GTGA:G	donor_gain	1.0000
20:63305559:GA:G	donor_gain	1.0000
20:63305561:G:GG	donor_gain	1.0000
20:63305879:A:AG	acceptor_gain	1.0000
20:63305880:G:GC	acceptor_gain	1.0000
20:63305880:GTT:G	acceptor_gain	1.0000
20:63305880:GTTGA:G	acceptor_gain	1.0000
20:63305988:GCTTC:G	donor_gain	1.0000
20:63306263:G:GT	donor_gain	1.0000
20:63306311:G:GT	donor_gain	1.0000
20:63306359:G:GT	donor_gain	1.0000
20:63307645:GTAG:G	donor_gain	1.0000
20:63309330:CA:C	acceptor_loss	1.0000
20:63309331:AGGTG:A	acceptor_loss	1.0000
20:63309332:G:T	acceptor_loss	1.0000
20:63311392:A:AG	acceptor_gain	1.0000
20:63311393:G:GA	acceptor_gain	1.0000
20:63311537:GAG:G	donor_gain	1.0000
20:63311744:GACCC:G	donor_gain	1.0000
20:63311749:G:GG	donor_gain	1.0000
20:63312922:G:T	donor_gain	1.0000
20:63313207:G:T	donor_gain	1.0000
20:63316551:AG:A	acceptor_gain	1.0000
20:63316552:GG:G	acceptor_gain	1.0000

AlphaMissense

8163 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:63313816:G:C	W761C	0.983
20:63313816:G:T	W761C	0.983
20:63313814:T:A	W761R	0.980
20:63313814:T:C	W761R	0.980
20:63307594:T:C	F201L	0.977
20:63307596:C:A	F201L	0.977
20:63307596:C:G	F201L	0.977
20:63312487:T:A	V624D	0.976
20:63307538:T:C	F182S	0.975
20:63297965:G:C	W46C	0.974
20:63297965:G:T	W46C	0.974
20:63305554:T:C	F111L	0.974
20:63305556:T:A	F111L	0.974
20:63305556:T:G	F111L	0.974
20:63307547:A:T	D185V	0.973
20:63311461:G:C	W487C	0.973
20:63311461:G:T	W487C	0.973
20:63307595:T:C	F201S	0.972
20:63307558:A:C	S189R	0.969
20:63307560:C:A	S189R	0.969
20:63307560:C:G	S189R	0.969
20:63309841:T:A	W397R	0.969
20:63309841:T:C	W397R	0.969
20:63311459:T:A	W487R	0.969
20:63311459:T:C	W487R	0.969
20:63308008:G:C	W231C	0.966
20:63308008:G:T	W231C	0.966
20:63314145:T:A	V811D	0.964
20:63309843:G:C	W397C	0.963
20:63309843:G:T	W397C	0.963

dbSNP variants (sampled 300 via entrez): RS1000003062 (20:63299787 T>C), RS1000019703 (20:63309036 G>A), RS1000022222 (20:63293779 CCT>C), RS1000073974 (20:63305109 G>A), RS1000196661 (20:63312883 G>A,C), RS1000360006 (20:63321420 C>A,G,T), RS1000366283 (20:63298905 G>A), RS1000412398 (20:63321111 G>A), RS1000542168 (20:63312223 G>A), RS1000735505 (20:63317076 G>A,T), RS1000785414 (20:63312258 T>A), RS1000836985 (20:63320470 G>A), RS1000993305 (20:63294437 C>T), RS1001001067 (20:63308283 G>A), RS1001003355 (20:63302379 G>T)

Disease associations

OMIM: gene MIM:619390 | disease phenotypes: MIM:148700, MIM:121200, MIM:613720

GenCC curated gene-disease

Disease	Classification	Inheritance
hereditary palmoplantar keratoderma	Limited	Autosomal dominant

Mondo (4): palmoplantar keratoderma i, striate, focal, or diffuse (MONDO:0007859), seizures, benign familial neonatal, 1 (MONDO:0007365), developmental and epileptic encephalopathy, 7 (MONDO:0013387), hereditary palmoplantar keratoderma (MONDO:0019272)

Orphanet (4): Diffuse palmoplantar keratoderma with painful fissures (Orphanet:369999), Focal palmoplantar keratoderma with joint keratoses (Orphanet:370002), Self-limited neonatal epilepsy (Orphanet:1949), KCNQ2-related developmental and epileptic encephalopathy (Orphanet:439218)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C567743	Epilepsy, Benign Neonatal, 1, And-Or Myokymia (supp.)
C536162	Keratosis palmoplantaris striata 1 (supp.)

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
sodium arsenite	increases expression	2
Benzo(a)pyrene	affects methylation	2
Cisplatin	affects cotreatment, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
calfactant	increases expression, affects cotreatment	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, increases expression	1
Copper	affects cotreatment, increases expression	1
Methapyrilene	decreases methylation	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Paclitaxel	affects cotreatment, increases expression	1
Okadaic Acid	increases expression	1
Nanotubes, Carbon	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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