C16orf90

Summary

C16orf90 (chromosome 16 open reading frame 90, HGNC:34455) is a protein-coding gene on chromosome 16p13.3, encoding Uncharacterized protein C16orf90 (A8MZG2).

At a glance

• Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Limited, GenCC)
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_001080524

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34455
Approved symbol	C16orf90
Name	chromosome 16 open reading frame 90
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC646174
Ensembl gene	ENSG00000215131
Ensembl biotype	protein_coding
Entrez	646174

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000399645, ENST00000437192

RefSeq mRNA: 2 — MANE Select: NM_001080524 NM_001080524, NM_001353385

CCDS: CCDS45397

Canonical transcript exons

ENST00000437192 — 3 exons

Exon	Start	End
ENSE00001539426	3493484	3493987
ENSE00001539428	3494524	3494877
ENSE00001696424	3495376	3495489

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 91.02.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0078 / max 6.7663, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156033	0.0045	2
207711	0.0033	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.02	gold quality
right testis	UBERON:0004534	90.90	gold quality
testis	UBERON:0000473	89.80	gold quality
apex of heart	UBERON:0002098	43.67	silver quality
bone marrow cell	CL:0002092	43.00	gold quality
granulocyte	CL:0000094	42.64	silver quality
blood	UBERON:0000178	38.73	silver quality
bone marrow	UBERON:0002371	37.76	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
muscle of leg	UBERON:0001383	36.07	gold quality
mucosa of stomach	UBERON:0001199	35.98	silver quality
cerebellum	UBERON:0002037	35.57	gold quality
gastrocnemius	UBERON:0001388	35.56	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
cerebellar cortex	UBERON:0002129	35.46	gold quality
cerebellar hemisphere	UBERON:0002245	35.27	gold quality
pituitary gland	UBERON:0000007	34.64	silver quality
heart left ventricle	UBERON:0002084	33.26	silver quality
right hemisphere of cerebellum	UBERON:0014890	33.19	gold quality
adult mammalian kidney	UBERON:0000082	33.09	silver quality
lymph node	UBERON:0000029	33.06	gold quality
prefrontal cortex	UBERON:0000451	33.03	silver quality
leukocyte	CL:0000738	32.83	gold quality
monocyte	CL:0000576	32.51	gold quality
right uterine tube	UBERON:0001302	32.45	gold quality
right lung	UBERON:0002167	32.26	gold quality
placenta	UBERON:0001987	32.20	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting C16orf90, 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-5193	100.00	67.26	1744
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-212-5P	96.83	67.43	950
HSA-MIR-4749-3P	96.40	66.24	798

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700037C18Rik	ENSMUSG00000005983
rattus_norvegicus	C10h16orf90	ENSRNOG00000007268

Protein

Protein identifiers

Uncharacterized protein C16orf90 — A8MZG2 (reviewed: A8MZG2)

All UniProt accessions (2): A8MZG2, H0Y3R3

RefSeq proteins (2): NP_001073993, NP_001340314 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027978	DUF4644	Family

Pfam: PF15486

UniProt features (7 total): region of interest 2, compositionally biased region 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MZG2-F1	54.52	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK, MARTENS_TRETINOIN_RESPONSE_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, MIR3119, MIR5193, MIR4726_3P, GSE13306_RA_VS_UNTREATED_TCONV_UP, GSE14308_TH17_VS_NATURAL_TREG_DN, GSE27786_LIN_NEG_VS_CD8_TCELL_DN, GSE27786_BCELL_VS_CD8_TCELL_DN, GSE411_UNSTIM_VS_100MIN_IL6_STIM_MACROPHAGE_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

174 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C16orf90	WFDC11	Q8NEX6	554
C16orf90	IQCF3	P0C7M6	480
C16orf90	SPANXN5	Q5MJ07	476
C16orf90	C3orf52	Q5BVD1	474
C16orf90	TP53TG5	Q9Y2B4	447
C16orf90	RGPD4	Q7Z3J3	440
C16orf90	DEFB112	Q30KQ8	434
C16orf90	FHIP2A	Q5W0V3	432
C16orf90	STARD6	P59095	430
C16orf90	GALNTL5	Q7Z4T8	411
C16orf90	PROCA1	Q8NCQ7	407
C16orf90	DNAJC5B	Q9UF47	398
C16orf90	SYDE2	Q5VT97	398
C16orf90	ZMYM5	Q9UJ78	376
C16orf90	CMSS1	Q9BQ75	375

IntAct

0 interactions, top by confidence:

BioGRID (2): C16orf90 (Affinity Capture-MS), C16orf90 (Negative Genetic)

ESM2 similar proteins: A0A1B0GUS0, A0A5F9ZHS7, A7E346, A7MB34, A8MZG2, B2RU40, D4A9R4, O08574, O75593, P0C1Z6, P0CG20, Q0VG99, Q0ZCJ7, Q17QH7, Q29RM2, Q2KIS6, Q2M2S6, Q2M3G4, Q2NL68, Q32LE6, Q3U1J1, Q5JXC2, Q5R815, Q5SW24, Q61660, Q63247, Q6NZ36, Q6PBC9, Q6ZN01, Q6ZRI6, Q7TN08, Q7Z591, Q80VF6, Q86WR7, Q8BG26, Q8BP99, Q8BXQ8, Q8IYS4, Q8N9Y4, Q8NAV2

Diamond homologs: A8MZG2, Q32LI1, Q8BT88

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

8 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

490 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3494688:CA:C	donor_gain	0.9900
16:3494308:C:CA	donor_gain	0.9800
16:3494359:G:C	donor_gain	0.9700
16:3494523:CCA:C	donor_gain	0.9700
16:3494772:C:A	donor_gain	0.9700
16:3495347:T:TA	donor_gain	0.9700
16:3495340:T:C	donor_gain	0.9600
16:3494715:T:A	donor_gain	0.9400
16:3494693:G:A	donor_gain	0.9300
16:3494532:C:A	donor_gain	0.9200
16:3494687:A:AC	donor_gain	0.9200
16:3494688:C:CC	donor_gain	0.9200
16:3493988:C:CC	acceptor_gain	0.9000
16:3494507:G:A	donor_gain	0.9000
16:3494331:C:A	donor_gain	0.8900
16:3495385:T:C	donor_gain	0.8900
16:3494322:CCG:C	donor_gain	0.8800
16:3494531:T:TA	donor_gain	0.8800
16:3495378:T:A	donor_gain	0.8800
16:3494689:A:AC	donor_gain	0.8600
16:3494690:C:CC	donor_gain	0.8600
16:3494771:T:TA	donor_gain	0.8600
16:3494878:C:CC	acceptor_gain	0.8500
16:3494877:TCT:T	acceptor_loss	0.8100
16:3494878:CT:C	acceptor_loss	0.8100
16:3494879:T:A	acceptor_loss	0.8100
16:3494431:GGCTT:G	acceptor_gain	0.8000
16:3494432:GCTTG:G	acceptor_gain	0.8000
16:3495292:C:A	donor_gain	0.8000
16:3494559:T:TA	donor_gain	0.7900

AlphaMissense

1171 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3495398:A:C	F8L	0.973
16:3495398:A:T	F8L	0.973
16:3495400:A:G	F8L	0.973
16:3494753:G:C	F57L	0.953
16:3494753:G:T	F57L	0.953
16:3494755:A:G	F57L	0.953
16:3494756:G:C	N56K	0.934
16:3494756:G:T	N56K	0.934
16:3494754:A:G	F57S	0.917
16:3494765:C:A	K53N	0.904
16:3494765:C:G	K53N	0.904
16:3494754:A:C	F57C	0.879
16:3494741:G:C	H61Q	0.877
16:3494741:G:T	H61Q	0.877
16:3493872:C:A	K172N	0.862
16:3493872:C:G	K172N	0.862
16:3494743:G:C	H61D	0.849
16:3494759:C:A	K55N	0.847
16:3494759:C:G	K55N	0.847
16:3495399:A:C	F8C	0.844
16:3495399:A:G	F8S	0.833
16:3493917:C:A	K157N	0.811
16:3493917:C:G	K157N	0.811
16:3494757:T:A	N56I	0.808
16:3494739:A:T	L62H	0.801
16:3494739:A:G	L62P	0.798
16:3495384:A:G	I13T	0.791
16:3494823:A:G	I34T	0.774
16:3494758:T:C	N56D	0.769
16:3494742:T:C	H61R	0.766

dbSNP variants (sampled 300 via entrez): RS1000420994 (16:3494006 A>G), RS1000452259 (16:3493770 C>T), RS1001140390 (16:3494707 G>C), RS1001596488 (16:3494353 C>T), RS1001969533 (16:3495264 G>A), RS1002025943 (16:3494088 G>C,T), RS1002340121 (16:3495451 C>G), RS1002615572 (16:3497437 T>C), RS1004024382 (16:3498640 A>C), RS1004558058 (16:3493542 C>T), RS1004875604 (16:3494396 G>A), RS1004877710 (16:3498595 G>C,T), RS1004927883 (16:3494631 C>T), RS1005211099 (16:3495503 G>C), RS1005260343 (16:3495751 G>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
multiple congenital anomalies/dysmorphic syndrome	Limited	Autosomal recessive

Mondo (1): multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
tebuconazole	decreases expression	1
Fulvestrant	increases methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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