C5orf15

Summary

C5orf15 (chromosome 5 open reading frame 15, HGNC:20656) is a protein-coding gene on chromosome 5q31.1, encoding Keratinocyte-associated transmembrane protein 2 (Q8NC54).

Predicted to be located in membrane.

Source: NCBI Gene 56951 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_020199

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20656
Approved symbol	C5orf15
Name	chromosome 5 open reading frame 15
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	KCT2, HTGN29
Ensembl gene	ENSG00000113583
Ensembl biotype	protein_coding
Entrez	56951

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000231512, ENST00000507191, ENST00000509913, ENST00000871985, ENST00000871986

RefSeq mRNA: 1 — MANE Select: NM_020199 NM_020199

CCDS: CCDS4167

Canonical transcript exons

ENST00000231512 — 3 exons

Exon	Start	End
ENSE00000763346	133959494	133960020
ENSE00001006700	133968446	133968625
ENSE00001679014	133955510	133956990

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 99.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 112.1344 / max 773.8396, expressed in 1824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63406	111.9567	1824
63407	0.1179	42
63408	0.0598	21

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibia	UBERON:0000979	99.33	gold quality
bronchial epithelial cell	CL:0002328	98.69	gold quality
germinal epithelium of ovary	UBERON:0001304	98.42	gold quality
palpebral conjunctiva	UBERON:0001812	98.29	gold quality
epithelium of nasopharynx	UBERON:0001951	98.29	gold quality
choroid plexus epithelium	UBERON:0003911	98.28	gold quality
nasopharynx	UBERON:0001728	98.27	gold quality
epithelium of bronchus	UBERON:0002031	98.04	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.97	gold quality
bronchus	UBERON:0002185	97.91	gold quality
eye	UBERON:0000970	97.89	gold quality
parietal pleura	UBERON:0002400	97.82	gold quality
pleura	UBERON:0000977	97.60	gold quality
cartilage tissue	UBERON:0002418	97.51	gold quality
visceral pleura	UBERON:0002401	97.46	gold quality
nephron tubule	UBERON:0001231	97.23	gold quality
renal medulla	UBERON:0000362	97.17	gold quality
renal glomerulus	UBERON:0000074	96.99	gold quality
metanephric glomerulus	UBERON:0004736	96.98	gold quality
kidney epithelium	UBERON:0004819	96.98	gold quality
synovial joint	UBERON:0002217	96.77	gold quality
nasal cavity mucosa	UBERON:0001826	96.76	gold quality
pigmented layer of retina	UBERON:0001782	96.72	gold quality
retina	UBERON:0000966	96.70	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.49	gold quality
endometrium	UBERON:0001295	96.42	gold quality
jejunal mucosa	UBERON:0000399	96.41	gold quality
nasal cavity epithelium	UBERON:0005384	96.37	gold quality
islet of Langerhans	UBERON:0000006	96.21	gold quality
epithelial cell of pancreas	CL:0000083	96.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting C5orf15, 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-5692A	100.00	74.40	6850
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch73-269m14.2	ENSDARG00000090747
mus_musculus	9530068E07Rik	ENSMUSG00000036275
rattus_norvegicus	C10h5orf15	ENSRNOG00000006148
caenorhabditis_elegans		WBGENE00011742

Protein

Protein identifiers

Keratinocyte-associated transmembrane protein 2 — Q8NC54 (reviewed: Q8NC54)

All UniProt accessions (1): Q8NC54

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Widely expressed.

RefSeq proteins (1): NP_064584* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037645	KCT2	Family

Pfam: PF17818

UniProt features (14 total): modified residue 2, sequence conflict 2, topological domain 2, region of interest 2, compositionally biased region 2, signal peptide 1, chain 1, glycosylation site 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NC54-F1	57.94	0.00

Functional residue map

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

Post-translational modifications (2): 256, 229

Glycosylation sites (1): 75

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 176 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, MARTINEZ_RB1_TARGETS_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, CYTAGCAAY_UNKNOWN, SCHLOSSER_SERUM_RESPONSE_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, MODULE_18, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MARTINEZ_RB1_AND_TP53_TARGETS_UP, LAIHO_COLORECTAL_CANCER_SERRATED_UP, PETRETTO_HEART_MASS_QTL_CIS_UP, chr5q31, RFX1_01, NUYTTEN_NIPP1_TARGETS_DN, BOQUEST_STEM_CELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

476 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C5orf15	FXYD5	Q96DB9	503
C5orf15	EFCAB8	A8MWE9	434
C5orf15	TMEM123	Q8N131	403
C5orf15	PHYKPL	Q8IUZ5	400
C5orf15	LDAF1	Q96B96	400
C5orf15	ZNF17	P17021	395
C5orf15	ZCCHC9	Q8N567	394
C5orf15	TMTC4	Q5T4D3	387
C5orf15	PIERCE1	Q5BN46	370
C5orf15	CCDC28A	Q8IWP9	370
C5orf15	KLHDC8A	Q8IYD2	370
C5orf15	C1orf115	Q9H7X2	370
C5orf15	PRPSAP1	Q14558	368
C5orf15	FAM234A	Q9H0X4	367
C5orf15	TMEM256	Q8N2U0	360

IntAct

27 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
KCNE3	RIOK3	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	PGRMC1	psi-mi:“MI:0914”(association)	0.350
	SNAP23	psi-mi:“MI:0914”(association)	0.350
LMP2	WWP2	psi-mi:“MI:0914”(association)	0.350
	HAX1	psi-mi:“MI:0914”(association)	0.350
NS3	C15orf61	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
C4BPA	SPAG6	psi-mi:“MI:0914”(association)	0.350
KCNE3	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SLC1A1	UBXN8	psi-mi:“MI:0914”(association)	0.350
IL20RB	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
MAGEA8	B4GALT5	psi-mi:“MI:0914”(association)	0.350
SPPL2B	POC1B-GALNT4	psi-mi:“MI:0914”(association)	0.350
SLC12A9	PGRMC1	psi-mi:“MI:0914”(association)	0.350
SLC35G1	FAM234B	psi-mi:“MI:0914”(association)	0.350
SLC4A1	UPK3BL1	psi-mi:“MI:0914”(association)	0.350
SVOP	PGRMC1	psi-mi:“MI:0914”(association)	0.350
KRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
KCNK3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (40): C5orf15 (Affinity Capture-MS), C5orf15 (Synthetic Lethality), C5orf15 (Affinity Capture-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Affinity Capture-MS), C5orf15 (Affinity Capture-MS), C5orf15 (Affinity Capture-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS), C5orf15 (Proximity Label-MS)

ESM2 similar proteins: A0JPB5, A2A699, A5PLA0, A6QPA0, A8MVW0, B0BN44, B4DS77, D3ZZP4, O35451, P04921, P28906, Q06186, Q08DP3, Q08EA8, Q13113, Q1LVN1, Q28270, Q5F3A4, Q5FVQ7, Q5HZE8, Q5R5B8, Q60846, Q640B5, Q64314, Q7TNI2, Q810F0, Q86VZ4, Q8C4Q9, Q8CB67, Q8IUW5, Q8K064, Q8K201, Q8K2J7, Q8NC54, Q8NEA5, Q8R138, Q8TBP5, Q8WWG9, Q96L08, Q99941

Diamond homologs: O43493, P19814, Q5R5B8, Q62313, Q62314, Q8NC54, Q8K201

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

626 predictions. Top by Δscore:

Variant	Effect	Δscore
5:133959576:T:TA	donor_gain	1.0000
5:133959619:A:AC	donor_gain	1.0000
5:133959620:C:CC	donor_gain	1.0000
5:133959651:T:TA	donor_gain	1.0000
5:133968445:CCA:C	donor_gain	1.0000
5:133959637:AACC:A	donor_gain	0.9900
5:133960016:TACAA:T	acceptor_gain	0.9900
5:133960018:CAA:C	acceptor_gain	0.9900
5:133960021:C:CC	acceptor_gain	0.9900
5:133968560:T:TA	donor_gain	0.9900
5:133968664:C:A	donor_gain	0.9900
5:133957006:CAT:C	acceptor_gain	0.9800
5:133957008:T:TC	acceptor_gain	0.9800
5:133959577:C:A	donor_gain	0.9800
5:133968438:C:A	donor_gain	0.9800
5:133968559:AT:A	donor_gain	0.9800
5:133968663:T:TA	donor_gain	0.9800
5:133956990:TC:T	acceptor_loss	0.9700
5:133956991:C:CC	acceptor_gain	0.9700
5:133956991:CTGGA:C	acceptor_loss	0.9700
5:133956992:T:C	acceptor_loss	0.9700
5:133959620:CTGTT:C	donor_gain	0.9700
5:133959630:T:TA	donor_gain	0.9700
5:133960805:CTATT:C	donor_gain	0.9700
5:133967249:T:TA	donor_gain	0.9700
5:133959313:AAG:A	donor_gain	0.9600
5:133959492:ACCTT:A	donor_gain	0.9600
5:133959493:CCTTC:C	donor_gain	0.9600
5:133959496:T:A	donor_gain	0.9600
5:133967391:TA:T	donor_gain	0.9600

AlphaMissense

1746 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:133956862:A:C	F265L	0.996
5:133956862:A:T	F265L	0.996
5:133956864:A:G	F265L	0.996
5:133956930:A:G	Y243H	0.995
5:133959500:T:A	K220N	0.995
5:133959500:T:G	K220N	0.995
5:133959535:A:G	C209R	0.995
5:133959528:G:T	A211D	0.994
5:133956896:A:G	M254T	0.992
5:133959501:T:A	K220I	0.992
5:133959540:G:T	A207D	0.992
5:133959552:A:G	L203P	0.992
5:133956929:T:C	Y243C	0.991
5:133959508:G:C	H218D	0.991
5:133956920:A:T	L246Q	0.988
5:133959522:A:T	V213D	0.988
5:133956895:C:A	M254I	0.987
5:133956895:C:G	M254I	0.987
5:133956895:C:T	M254I	0.987
5:133956863:A:C	F265C	0.986
5:133956863:A:G	F265S	0.986
5:133956878:G:A	T260I	0.986
5:133956920:A:G	L246P	0.986
5:133959507:T:G	H218P	0.986
5:133956961:C:A	W232C	0.985
5:133956961:C:G	W232C	0.985
5:133959520:A:C	Y214D	0.985
5:133956923:C:G	R245P	0.983
5:133956929:T:G	Y243S	0.982
5:133956887:A:G	L257S	0.981

dbSNP variants (sampled 300 via entrez): RS1000234126 (5:133964819 A>C), RS1000753757 (5:133961231 G>A,T), RS1001084276 (5:133966502 T>A), RS1001205621 (5:133966119 G>A,T), RS1001421390 (5:133967814 A>G), RS1001577982 (5:133968025 C>A,G), RS1001715972 (5:133961463 G>A), RS1001910017 (5:133969048 T>A), RS1001936568 (5:133962901 A>G), RS1002178318 (5:133967612 T>C), RS1002449803 (5:133963236 A>G), RS1002466036 (5:133960330 T>C), RS1002785647 (5:133964517 G>A), RS1002815746 (5:133956758 C>A,T), RS1003133401 (5:133957173 T>A)

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
GCST000253_13	Attention deficit hyperactivity disorder and conduct disorder	8.000000e-06
GCST002337_33	Amyotrophic lateral sclerosis (sporadic)	7.000000e-08
GCST003075_123	Cognitive decline rate in late mild cognitive impairment	7.000000e-06
GCST003075_40	Cognitive decline rate in late mild cognitive impairment	9.000000e-07
GCST004866_13	Alopecia areata	9.000000e-07
GCST006408_12	Allergic sensitization	1.000000e-07
GCST007843_9	Rheumatoid arthritis	2.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007710	cognitive decline measurement
EFO:0005298	allergic sensitization measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
oxidized-L-alpha-1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine	affects expression, increases reaction	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Vehicle Emissions	affects expression, increases reaction	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ketoconazole	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Vinblastine	affects response to substance	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	affects expression, increases reaction	1

Clinical trials (associated diseases)

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