C20orf96

Summary

C20orf96 (chromosome 20 open reading frame 96, HGNC:16227) is a protein-coding gene on chromosome 20p13, encoding Uncharacterized protein C20orf96 (Q9NUD7).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 40 total — 2 pathogenic, 2 likely-pathogenic
• MANE Select transcript: NM_153269

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16227
Approved symbol	C20orf96
Name	chromosome 20 open reading frame 96
Location	20p13
Locus type	gene with protein product
Status	Approved
Aliases	dJ1103G7.2
Ensembl gene	ENSG00000196476
Ensembl biotype	protein_coding
Entrez	140680

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000360321, ENST00000382369, ENST00000400269, ENST00000907056

RefSeq mRNA: 2 — MANE Select: NM_153269 NM_080571, NM_153269

CCDS: CCDS12994, CCDS74685

Canonical transcript exons

ENST00000360321 — 11 exons

Exon	Start	End
ENSE00000858527	275968	276086
ENSE00000858528	279172	279330
ENSE00000858529	283963	284081
ENSE00000906672	277044	277145
ENSE00000906673	277226	277383
ENSE00000906674	278330	278429
ENSE00001241274	276793	276879
ENSE00001366163	270863	271267
ENSE00001644154	289559	289676
ENSE00001757661	290259	290307
ENSE00002270422	290591	290750

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 97.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.5306 / max 143.1427, expressed in 1711 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
185957	8.7960	1669
185960	1.0369	547
185958	0.3966	193
185959	0.3010	124

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.59	gold quality
left testis	UBERON:0004533	91.32	gold quality
right testis	UBERON:0004534	90.67	gold quality
testis	UBERON:0000473	88.03	gold quality
adenohypophysis	UBERON:0002196	87.36	gold quality
right ovary	UBERON:0002118	87.35	gold quality
left ovary	UBERON:0002119	87.28	gold quality
mucosa of transverse colon	UBERON:0004991	86.77	gold quality
metanephros cortex	UBERON:0010533	86.70	gold quality
left lobe of thyroid gland	UBERON:0001120	86.63	gold quality
right lobe of thyroid gland	UBERON:0001119	86.24	gold quality
endocervix	UBERON:0000458	85.90	gold quality
body of uterus	UBERON:0009853	85.62	gold quality
thyroid gland	UBERON:0002046	85.03	gold quality
pituitary gland	UBERON:0000007	84.62	gold quality
cortical plate	UBERON:0005343	84.50	gold quality
right adrenal gland cortex	UBERON:0035827	84.42	gold quality
left adrenal gland cortex	UBERON:0035825	83.85	gold quality
right adrenal gland	UBERON:0001233	83.84	gold quality
caudate nucleus	UBERON:0001873	83.68	gold quality
nucleus accumbens	UBERON:0001882	83.61	gold quality
ganglionic eminence	UBERON:0004023	83.56	gold quality
left adrenal gland	UBERON:0001234	83.55	gold quality
ventricular zone	UBERON:0003053	83.38	gold quality
hypothalamus	UBERON:0001898	83.35	gold quality
transverse colon	UBERON:0001157	83.31	gold quality
left uterine tube	UBERON:0001303	83.26	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.18	gold quality
apex of heart	UBERON:0002098	83.07	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.99
E-MTAB-6386	no	106.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting C20orf96, 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-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	6820408C15Rik	ENSMUSG00000032680
rattus_norvegicus	C3h20orf96	ENSRNOG00000023721

Protein

Protein identifiers

Uncharacterized protein C20orf96 — Q9NUD7 (reviewed: Q9NUD7)

All UniProt accessions (3): Q9NUD7, F5GZA9, Q5JYC3

RefSeq proteins (2): NP_542138, NP_695001* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029236	DUF4618	Family

Pfam: PF15397

UniProt features (3 total): chain 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUD7-F1	76.23	0.51

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): MIKKELSEN_MCV6_LCP_WITH_H3K4ME3, MIKKELSEN_MEF_LCP_WITH_H3K4ME3, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, MIKKELSEN_ES_LCP_WITH_H3K4ME3, MIKKELSEN_NPC_LCP_WITH_H3K4ME3, FOXN3_TARGET_GENES, HHEX_TARGET_GENES, PITX1_TARGET_GENES, RYBP_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF362_TARGET_GENES, ZNF407_TARGET_GENES, MIR4728_5P, MIR6785_5P

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1033 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C20orf96	SHLD2	Q86V20	692
C20orf96	SHLD3	Q6ZNX1	648
C20orf96	MAD2L2	Q9UI95	526
C20orf96	KDM4C	Q9H3R0	461
C20orf96	SHLD1	Q8IYI0	443
C20orf96	TCP10L	Q8TDR4	415
C20orf96	LGALS16	A8MUM7	399
C20orf96	SLC9D1	Q6UWJ1	368
C20orf96	SPATA20	Q8TB22	364
C20orf96	CCDC14	Q49A88	357
C20orf96	MTFR1	Q15390	332
C20orf96	CEP295	Q9C0D2	327
C20orf96	SLC45A1	Q9Y2W3	319
C20orf96	ZCCHC3	Q9NUD5	317
C20orf96	UACA	Q9BZF9	316

IntAct

5 interactions, top by confidence:

A	B	Type	Score
C20orf96	CFAP74	psi-mi:“MI:0915”(physical association)	0.560
C20orf96	HSPA8	psi-mi:“MI:0914”(association)	0.350
C20orf96	VWA8	psi-mi:“MI:0914”(association)	0.350
TRAF3IP1	C20orf96	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): TYW5 (Affinity Capture-MS), ALOXE3 (Affinity Capture-MS), CFAP74 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), KIAA0391 (Affinity Capture-MS), CAMK2B (Affinity Capture-MS), DARS2 (Affinity Capture-MS), VWA8 (Affinity Capture-MS), PCCA (Affinity Capture-MS), BCKDK (Affinity Capture-MS), TARS2 (Affinity Capture-MS), RSAD1 (Affinity Capture-MS), PTCD1 (Affinity Capture-MS), GATB (Affinity Capture-MS), C20orf96 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A087WRI3, A2BFC9, A2RRW4, A4QMS7, A6NJV1, A6NL82, A6QPC0, A6QQ68, A8E4X8, A8E5W8, A8QW39, A9JS51, D6REC4, F1P3Y5, G3X6E2, P0C875, Q0VB26, Q1MSJ5, Q2IA00, Q2T9Q3, Q2TA11, Q3UY96, Q494V2, Q497Q6, Q4KKZ1, Q4QR77, Q4R5Y0, Q4R8V8, Q5NC57, Q5ZIH9, Q6J272, Q6PII3, Q6ZQR2, Q6ZVS7, Q7Z4T9, Q8CFW7, Q8N1D5, Q8N6G2, Q8WW14, Q95LR0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	2
Uncertain significance	11
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
146085	GRCh38/hg38 20p13(chr20:89939-364235)x1	Pathogenic
442856	GRCh37/hg19 20p13(chr20:61568-431502)x1	Pathogenic
1526675	GRCh37/hg19 20p13(chr20:61568-806878)	Likely pathogenic
979574	GRCh37/hg19 20p13(chr20:61568-677437)x1	Likely pathogenic

SpliceAI

1548 predictions. Top by Δscore:

Variant	Effect	Δscore
20:275966:A:AC	donor_gain	1.0000
20:275967:C:CC	donor_gain	1.0000
20:276778:T:TA	donor_gain	1.0000
20:276791:A:AC	donor_gain	1.0000
20:276792:C:CC	donor_gain	1.0000
20:276792:CTTCT:C	donor_gain	1.0000
20:276794:T:TA	donor_gain	1.0000
20:277038:ACT:A	donor_loss	1.0000
20:277039:CTCA:C	donor_loss	1.0000
20:277041:C:CG	donor_loss	1.0000
20:277042:A:AC	donor_gain	1.0000
20:277042:ACCG:A	donor_gain	1.0000
20:277043:C:CT	donor_gain	1.0000
20:277043:CCG:C	donor_gain	1.0000
20:277043:CCGC:C	donor_gain	1.0000
20:277142:CATC:C	acceptor_gain	1.0000
20:277144:TC:T	acceptor_gain	1.0000
20:277145:CC:C	acceptor_gain	1.0000
20:277146:C:CC	acceptor_gain	1.0000
20:277146:C:G	acceptor_loss	1.0000
20:277147:T:A	acceptor_loss	1.0000
20:277155:A:T	acceptor_gain	1.0000
20:277221:CCTA:C	donor_loss	1.0000
20:277225:CC:C	donor_loss	1.0000
20:277242:A:C	donor_gain	1.0000
20:277298:ATGGT:A	donor_gain	1.0000
20:277380:AGAT:A	acceptor_gain	1.0000
20:277382:ATCTG:A	acceptor_loss	1.0000
20:277383:TCTGG:T	acceptor_loss	1.0000
20:277384:C:CC	acceptor_gain	1.0000

AlphaMissense

2423 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:275994:A:C	F335L	0.970
20:275994:A:T	F335L	0.970
20:275996:A:G	F335L	0.970
20:271266:A:G	C345R	0.932
20:277251:A:G	L233P	0.916
20:271210:G:C	F363L	0.909
20:271210:G:T	F363L	0.909
20:271212:A:G	F363L	0.909
20:277359:A:G	L197P	0.900
20:271264:G:C	C345W	0.893
20:276031:A:G	L323P	0.883
20:277263:A:G	L229P	0.883
20:271265:C:G	C345S	0.882
20:271266:A:T	C345S	0.882
20:278368:A:G	L176P	0.881
20:279251:A:G	L129P	0.874
20:275995:A:C	F335C	0.870
20:277117:C:G	R251P	0.854
20:277138:A:G	L244P	0.854
20:277257:C:G	R231P	0.851
20:275995:A:G	F335S	0.850
20:275996:A:T	F335I	0.850
20:271241:A:T	L353H	0.846
20:277319:G:C	F210L	0.843
20:277319:G:T	F210L	0.843
20:277321:A:G	F210L	0.843
20:275998:A:T	I334K	0.842
20:277129:A:G	L247P	0.842
20:277317:A:G	L211P	0.839
20:279203:C:G	R145P	0.838

dbSNP variants (sampled 300 via entrez): RS1000052997 (20:277500 G>A), RS1000058930 (20:280039 G>T), RS1000130577 (20:278713 G>A,C), RS1000257796 (20:272079 TA>T,TAA), RS1000326942 (20:280229 T>C), RS1000691921 (20:271777 T>A,C), RS1000747401 (20:270843 C>A,T), RS1000836080 (20:276340 A>G), RS1000875979 (20:287221 T>C), RS1000885723 (20:285707 G>A,C), RS1001370812 (20:292586 G>A), RS1001624269 (20:275726 C>A,T), RS1001682120 (20:281294 C>A,G), RS1001749760 (20:287041 T>C), RS1001879917 (20:283085 T>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST007010_4	Logical memory (delayed recall)	6.000000e-07
GCST007011_4	Logical memory (immediate recall)	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
lead acetate	decreases expression	1
butyraldehyde	increases expression	1
potassium chromate(VI)	decreases expression	1
cupric chloride	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Diethylhexyl Phthalate	decreases expression	1
Smoke	increases abundance, increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice