C16orf54

Summary

C16orf54 (chromosome 16 open reading frame 54, HGNC:26649) is a protein-coding gene on chromosome 16p11.2, encoding Transmembrane protein C16orf54 (Q6UWD8).

Predicted to be located in membrane.

Source: NCBI Gene 283897 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 7 total — 2 pathogenic
• MANE Select transcript: NM_175900

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26649
Approved symbol	C16orf54
Name	chromosome 16 open reading frame 54
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35681, SAIL
Ensembl gene	ENSG00000185905
Ensembl biotype	protein_coding
Entrez	283897

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000329410, ENST00000961953

RefSeq mRNA: 1 — MANE Select: NM_175900 NM_175900

CCDS: CCDS10652

Canonical transcript exons

ENST00000329410 — 2 exons

Exon	Start	End
ENSE00001299431	29745911	29745990
ENSE00001301136	29742463	29744951

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 96.44.

FANTOM5 (CAGE): breadth broad, TPM avg 19.8661 / max 892.4886, expressed in 475 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156948	19.7862	475
156947	0.0800	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelium of nasopharynx	UBERON:0001951	96.44	gold quality
bone marrow cell	CL:0002092	96.18	gold quality
blood	UBERON:0000178	95.72	gold quality
granulocyte	CL:0000094	94.03	gold quality
bone marrow	UBERON:0002371	93.71	gold quality
leukocyte	CL:0000738	89.71	gold quality
monocyte	CL:0000576	89.06	gold quality
thymus	UBERON:0002370	88.30	gold quality
trabecular bone tissue	UBERON:0002483	87.48	gold quality
lymph node	UBERON:0000029	84.64	gold quality
vermiform appendix	UBERON:0001154	84.39	gold quality
spleen	UBERON:0002106	82.38	gold quality
bronchial epithelial cell	CL:0002328	78.37	gold quality
palpebral conjunctiva	UBERON:0001812	78.18	gold quality
bronchus	UBERON:0002185	77.86	gold quality
caecum	UBERON:0001153	76.12	gold quality
mucosa of paranasal sinus	UBERON:0005030	75.98	gold quality
nasal cavity mucosa	UBERON:0001826	75.65	gold quality
amniotic fluid	UBERON:0000173	75.50	gold quality
tonsil	UBERON:0002372	75.44	gold quality
superficial temporal artery	UBERON:0001614	75.33	gold quality
oviduct epithelium	UBERON:0004804	74.99	gold quality
lower lobe of lung	UBERON:0008949	74.63	gold quality
skin of hip	UBERON:0001554	74.59	gold quality
visceral pleura	UBERON:0002401	72.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.70	silver quality
parietal pleura	UBERON:0002400	71.95	gold quality
pylorus	UBERON:0001166	71.75	gold quality
nasal cavity epithelium	UBERON:0005384	71.06	silver quality
rectum	UBERON:0001052	70.51	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	215.73
E-GEOD-135922	yes	22.05
E-ANND-3	yes	20.77
E-CURD-89	no	171.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RUNX1

miRNA regulators (miRDB)

79 targeting C16orf54, 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-3613-3P	100.00	76.36	7965
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-149-3P	99.72	68.22	3963
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-6779-5P	99.70	65.76	2363
HSA-MIR-1283	99.69	72.42	3009

Literature-anchored findings (GeneRIF, showing 1)

• Integrated Analysis of C16orf54 as a Potential Prognostic, Diagnostic, and Immune Marker across Pan-Cancer. (PMID:36118669)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	AI467606	ENSMUSG00000045165
rattus_norvegicus	C1h16orf54	ENSRNOG00000016978

Protein

Protein identifiers

Transmembrane protein C16orf54 — Q6UWD8 (reviewed: Q6UWD8)

All UniProt accessions (1): Q6UWD8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Post-translational modifications. O-glycosylated with core 1 or possibly core 8 glycans.

RefSeq proteins (1): NP_787096* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031499	DUF4689	Family

Pfam: PF15755

UniProt features (9 total): modified residue 3, region of interest 2, chain 1, transmembrane region 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWD8-F1	60.10	0.10

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 (3): 112, 116, 194

Glycosylation sites (1): 4

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 118 (showing top): chr16p11, YAMASHITA_METHYLATED_IN_PROSTATE_CANCER, MIKKELSEN_ES_ICP_WITH_H3K4ME3, PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP, YANG_BCL3_TARGETS_UP, PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN, NFKBIA_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR1283, MIR9_5P, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, GSE10239_NAIVE_VS_DAY4.5_EFF_CD8_TCELL_UP

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf54	ASPHD1	Q5U4P2	804
C16orf54	QPRT	Q15274	715
C16orf54	FIMP1	Q96LL3	692
C16orf54	CDIPT	O14735	670
C16orf54	HIRIP3	Q9BW71	664
C16orf54	TMEM219	Q86XT9	662
C16orf54	SEZ6L2	Q6UXD5	609
C16orf54	KCTD13	Q8WZ19	602
C16orf54	DOC2A	Q14183	600
C16orf54	YPEL3	P61236	598
C16orf54	INO80E	Q8NBZ0	596
C16orf54	PAGR1	Q9BTK6	594
C16orf54	TAOK2	Q9UL54	585
C16orf54	TLCD3B	Q71RH2	545
C16orf54	KIF22	Q14807	542

IntAct

27 interactions, top by confidence:

A	B	Type	Score
C16orf54	ANKRD46	psi-mi:“MI:0915”(physical association)	0.560
CLDN11	C16orf54	psi-mi:“MI:0915”(physical association)	0.560
C16orf54	RPRM	psi-mi:“MI:0915”(physical association)	0.560
C16orf54	SEC22A	psi-mi:“MI:0915”(physical association)	0.560
C16orf54	LPAR3	psi-mi:“MI:0915”(physical association)	0.560
PMP22	C16orf54	psi-mi:“MI:0915”(physical association)	0.560
ATXN3	C16orf54	psi-mi:“MI:0915”(physical association)	0.560
C16orf54	IFNA17	psi-mi:“MI:0914”(association)	0.530
LHFPL4	IFNA17	psi-mi:“MI:0914”(association)	0.530
AP2B1	C16orf54	psi-mi:“MI:0407”(direct interaction)	0.440
C16orf54	TNFSF9	psi-mi:“MI:0914”(association)	0.350
CLDN11	C16orf54	psi-mi:“MI:0915”(physical association)	0.000
RPRM	C16orf54	psi-mi:“MI:0915”(physical association)	0.000
PMP22	C16orf54	psi-mi:“MI:0915”(physical association)	0.000
ANKRD46	C16orf54	psi-mi:“MI:0915”(physical association)	0.000
SEC22A	C16orf54	psi-mi:“MI:0915”(physical association)	0.000
LPAR3	C16orf54	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): IFNA17 (Affinity Capture-MS), EFNB1 (Affinity Capture-MS), PKP4 (Affinity Capture-MS), C16orf54 (Two-hybrid), C16orf54 (Two-hybrid), C16orf54 (Two-hybrid), C16orf54 (Two-hybrid), C16orf54 (Two-hybrid), ANKRD46 (Two-hybrid), C16orf54 (Affinity Capture-MS), IFNA17 (Affinity Capture-MS), PIK3R3 (Affinity Capture-MS), EFNB1 (Affinity Capture-MS), TNFSF9 (Affinity Capture-MS), DDR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQS6, A0A1B0GUA5, A0A2R8YCJ5, A2VDX9, A5A769, A5PJP1, A6NGB7, A6NKF7, A8MVW0, B2RU40, C9JH25, C9JTQ0, D4A9R4, O15049, P0C7N4, P0DPE3, P98162, Q0VD38, Q14761, Q1HCM0, Q29RM6, Q32M26, Q3LUD3, Q3TYP4, Q3UPH7, Q5BK39, Q5BLP8, Q5JTB6, Q5RCL0, Q64322, Q64697, Q6F5E0, Q6NUJ2, Q6NZ36, Q6QNY0, Q6UWD8, Q8C708, Q8C7U1, Q8K071, Q8K262

Diamond homologs: Q5BK39, Q6UWD8, Q8C708

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2580312	GRCh37/hg19 16p11.2(chr16:29511270-30243006)x1	Pathogenic
2685568	GRCh37/hg19 16p11.2(chr16:29343245-30240227)x1	Pathogenic

SpliceAI

243 predictions. Top by Δscore:

Variant	Effect	Δscore
16:29745906:CTCA:C	donor_loss	0.9700
16:29745907:TCA:T	donor_loss	0.9700
16:29745908:CA:C	donor_loss	0.9700
16:29745910:C:CA	donor_loss	0.9700
16:29745904:AACTC:A	donor_loss	0.9600
16:29745905:ACTCA:A	donor_loss	0.9600
16:29744951:TC:T	acceptor_loss	0.9500
16:29744952:C:G	acceptor_loss	0.9500
16:29744953:T:A	acceptor_loss	0.9500
16:29745909:A:AC	donor_gain	0.9400
16:29745910:C:CC	donor_gain	0.9400
16:29744952:C:CC	acceptor_gain	0.9300
16:29744949:CAT:C	acceptor_gain	0.9200
16:29744962:C:CT	acceptor_gain	0.9200
16:29745954:T:TA	donor_gain	0.9200
16:29744960:C:CT	acceptor_gain	0.9100
16:29745903:CAACT:C	donor_loss	0.9100
16:29744963:A:T	acceptor_gain	0.8500
16:29745537:T:A	acceptor_gain	0.8500
16:29745909:AC:A	donor_gain	0.8500
16:29745910:CC:C	donor_gain	0.8500
16:29745663:T:TA	donor_gain	0.8400
16:29744950:ATCT:A	acceptor_gain	0.8300
16:29745625:C:A	donor_gain	0.8200
16:29744948:GCAT:G	acceptor_gain	0.8000
16:29744949:CATC:C	acceptor_gain	0.8000
16:29744947:GGCAT:G	acceptor_gain	0.7500
16:29744954:G:C	acceptor_loss	0.7500
16:29745609:C:A	donor_gain	0.7500
16:29744951:TCTG:T	acceptor_gain	0.7400

AlphaMissense

1407 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:29744313:G:C	F213L	0.993
16:29744313:G:T	F213L	0.993
16:29744315:A:G	F213L	0.993
16:29744310:C:A	W214C	0.989
16:29744310:C:G	W214C	0.989
16:29744314:A:G	F213S	0.986
16:29744323:A:G	I210T	0.982
16:29744314:A:C	F213C	0.981
16:29744323:A:C	I210S	0.981
16:29744709:C:A	W81C	0.981
16:29744709:C:G	W81C	0.981
16:29744355:C:A	W199C	0.979
16:29744355:C:G	W199C	0.979
16:29744730:C:A	W74C	0.978
16:29744730:C:G	W74C	0.978
16:29744312:A:G	W214R	0.977
16:29744312:A:T	W214R	0.977
16:29744667:C:A	W95C	0.974
16:29744667:C:G	W95C	0.974
16:29744357:A:G	W199R	0.970
16:29744357:A:T	W199R	0.970
16:29744711:A:G	W81R	0.970
16:29744711:A:T	W81R	0.970
16:29744323:A:T	I210N	0.966
16:29744311:C:G	W214S	0.965
16:29744669:A:G	W95R	0.963
16:29744669:A:T	W95R	0.963
16:29744732:A:G	W74R	0.963
16:29744732:A:T	W74R	0.963
16:29744499:G:C	F151L	0.961

dbSNP variants (sampled 300 via entrez): RS1000595169 (16:29743035 C>T), RS1000639186 (16:29746141 G>A,T), RS1000755061 (16:29746404 T>A,C), RS1000985062 (16:29747297 T>C), RS1001253009 (16:29745771 C>T), RS1001690916 (16:29743507 C>A,T), RS1002172723 (16:29747909 T>C), RS1002256829 (16:29746924 GTCTC>G,GTC,GTCTCTC), RS1002312836 (16:29746648 C>A), RS1002596878 (16:29747664 G>T), RS1002996755 (16:29744627 C>T), RS1003090653 (16:29742146 T>C), RS1005826174 (16:29746596 G>A,T), RS1005854430 (16:29746817 C>T), RS1007374081 (16:29747015 A>T)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenite	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression, affects response to substance, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Diuron	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Nickel	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	increases abundance, increases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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