C4orf36

Summary

C4orf36 (chromosome 4 open reading frame 36, HGNC:28386) is a protein-coding gene on chromosome 4q21.3, encoding Uncharacterized protein C4orf36 (Q96KX1).

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_144645

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28386
Approved symbol	C4orf36
Name	chromosome 4 open reading frame 36
Location	4q21.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC26744
Ensembl gene	ENSG00000163633
Ensembl biotype	protein_coding
OMIM	621278
Entrez	132989

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000295898, ENST00000462714, ENST00000504008, ENST00000504371, ENST00000506308, ENST00000512468, ENST00000904796, ENST00000904797, ENST00000904798, ENST00000913350, ENST00000913351, ENST00000941964

RefSeq mRNA: 7 — MANE Select: NM_144645 NM_001369888, NM_001369889, NM_001414635, NM_001414636, NM_001414638, NM_001414640, NM_144645

CCDS: CCDS3615

Canonical transcript exons

ENST00000295898 — 5 exons

Exon	Start	End
ENSE00001196777	86876205	86876443
ENSE00001196789	86892183	86892422
ENSE00001322383	86887758	86887893
ENSE00003815117	86891456	86891593
ENSE00003823946	86888121	86888275

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 81.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1649 / max 8.1195, expressed in 66 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
52990	0.1305	45
52989	0.0344	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.87	gold quality
right testis	UBERON:0004534	77.83	gold quality
left testis	UBERON:0004533	77.70	gold quality
testis	UBERON:0000473	77.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.71	gold quality
cortical plate	UBERON:0005343	68.90	gold quality
esophagus mucosa	UBERON:0002469	68.19	gold quality
lower esophagus mucosa	UBERON:0035834	67.05	gold quality
stromal cell of endometrium	CL:0002255	67.02	gold quality
skin of abdomen	UBERON:0001416	66.21	gold quality
right lung	UBERON:0002167	66.06	gold quality
endocervix	UBERON:0000458	65.85	gold quality
prefrontal cortex	UBERON:0000451	64.91	gold quality
zone of skin	UBERON:0000014	64.53	gold quality
left ovary	UBERON:0002119	64.35	gold quality
endometrium	UBERON:0001295	64.34	gold quality
vagina	UBERON:0000996	63.70	gold quality
ectocervix	UBERON:0012249	63.59	gold quality
ovary	UBERON:0000992	63.46	gold quality
skin of leg	UBERON:0001511	63.38	gold quality
prostate gland	UBERON:0002367	62.24	gold quality
superior frontal gyrus	UBERON:0002661	62.00	gold quality
right ovary	UBERON:0002118	61.80	gold quality
uterine cervix	UBERON:0000002	61.75	gold quality
thoracic mammary gland	UBERON:0005200	61.62	gold quality
thyroid gland	UBERON:0002046	61.48	gold quality
left lobe of thyroid gland	UBERON:0001120	61.32	gold quality
frontal cortex	UBERON:0001870	61.22	gold quality
right lobe of thyroid gland	UBERON:0001119	60.81	gold quality
urinary bladder	UBERON:0001255	60.57	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6058	no	8.48
E-ANND-3	no	1.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting C4orf36, 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-4682	100.00	68.89	1258
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-6509-3P	98.32	67.33	1343
HSA-MIR-665	97.60	65.64	1781
HSA-MIR-4486	96.96	60.61	931
HSA-MIR-4436B-5P	96.71	68.37	1346

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700016H13Rik	ENSMUSG00000029320
rattus_norvegicus	C14h4orf36	ENSRNOG00000060245

Protein

Protein identifiers

Uncharacterized protein C4orf36 — Q96KX1 (reviewed: Q96KX1)

All UniProt accessions (5): Q96KX1, D6RAE1, D6RCP1, D6RF10, D6RGW9

RefSeq proteins (7): NP_001356817, NP_001356818, NP_001401564, NP_001401565, NP_001401567, NP_001401569, NP_653246* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027825	DUF4522	Family

Pfam: PF15022

UniProt features (3 total): sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KX1-F1	77.06	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): chr4q21, TGGAAA_NFAT_Q4_01, CAMPS_COLON_CANCER_COPY_NUMBER_UP, BCAT_BILD_ET_AL_UP, ATF5_TARGET_GENES, FEV_TARGET_GENES, GREB1_TARGET_GENES, GUCY1B1_TARGET_GENES, LHX9_TARGET_GENES, TASOR_TARGET_GENES, ZNF618_TARGET_GENES, ZSCAN30_TARGET_GENES, GSE10239_NAIVE_VS_MEMORY_CD8_TCELL_DN, MIR6509_3P, MIR181A_2_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

58 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C4orf36	PRR27	Q6MZM9	630
C4orf36	CFAP299	Q6V702	611
C4orf36	ODAPH	Q17RF5	520
C4orf36	FDCSP	Q8NFU4	445
C4orf36	PGPEP1	Q9NXJ5	444
C4orf36	CSHL1	Q14406	400
C4orf36	DYNLT3	P51808	395
C4orf36	ODAM	A1E959	392
C4orf36	STATH	P02808	355
C4orf36	DYNLT1	P63172	289
C4orf36	A6NFB4	A6NFB4	245
C4orf36	MEDAG	Q5VYS4	226
C4orf36	RLN1	P04808	222
C4orf36	ST6GALNAC6	Q969X2	211
C4orf36	INSL4	Q14641	201

IntAct

0 interactions, top by confidence:

BioGRID (4): C4orf36 (Affinity Capture-MS), C4orf36 (Affinity Capture-MS), C4orf36 (Affinity Capture-MS), C4orf36 (Protein-peptide)

ESM2 similar proteins: A0A1B0GVR7, A0PJW8, A2BYT2, A5FRX9, B8G1X0, C1DKL7, G3UWD5, O42659, O62953, O95567, O98453, P05899, P11690, P11794, P19718, P20920, P27975, P32544, P33482, P39971, P52776, P54446, P69516, P69517, P86209, Q02781, Q0ABH1, Q1X6Y0, Q3AMN4, Q3J8R8, Q3K5Z2, Q3MFB7, Q3ZZM0, Q537H7, Q57P89, Q5I162, Q5PHY6, Q6AY31, Q75003, Q7CQJ0

Diamond homologs: Q6AY31, Q96KX1, Q9DAA3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1761 predictions. Top by Δscore:

Variant	Effect	Δscore
4:86887889:GATAG:G	acceptor_gain	1.0000
4:86887891:TAG:T	acceptor_gain	1.0000
4:86887893:GCTGA:G	acceptor_loss	1.0000
4:86887894:C:CC	acceptor_gain	1.0000
4:86887894:CTGAA:C	acceptor_loss	1.0000
4:86887895:T:A	acceptor_loss	1.0000
4:86888119:A:AC	donor_gain	1.0000
4:86888120:C:CC	donor_gain	1.0000
4:86888120:CATT:C	donor_gain	1.0000
4:86926250:C:A	donor_gain	1.0000
4:86887890:ATAG:A	acceptor_gain	0.9900
4:86887892:AG:A	acceptor_gain	0.9900
4:86888114:AACTT:A	donor_loss	0.9900
4:86888115:ACTT:A	donor_loss	0.9900
4:86888116:CTTAC:C	donor_loss	0.9900
4:86888117:TTACA:T	donor_loss	0.9900
4:86888118:TACA:T	donor_loss	0.9900
4:86888119:A:T	donor_loss	0.9900
4:86888120:CA:C	donor_gain	0.9900
4:86890782:A:AC	donor_gain	0.9900
4:86890783:C:CC	donor_gain	0.9900
4:86890828:CACGA:C	donor_gain	0.9900
4:86890835:T:TA	donor_gain	0.9900
4:86926226:A:AC	donor_gain	0.9900
4:86926227:C:CC	donor_gain	0.9900
4:86926242:TTG:T	donor_gain	0.9900
4:86926243:TGT:T	donor_gain	0.9900
4:86926249:T:TA	donor_gain	0.9900
4:86926253:T:TA	donor_gain	0.9900
4:86933393:A:AC	donor_gain	0.9900

AlphaMissense

749 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:86888238:A:G	W35R	0.884
4:86888238:A:T	W35R	0.884
4:86887781:T:A	R111S	0.876
4:86887781:T:G	R111S	0.876
4:86887860:C:G	R85P	0.859
4:86888203:G:C	F46L	0.853
4:86888203:G:T	F46L	0.853
4:86888205:A:G	F46L	0.853
4:86891500:T:A	R7S	0.833
4:86891500:T:G	R7S	0.833
4:86887778:T:A	R112S	0.810
4:86887778:T:G	R112S	0.810
4:86888185:A:C	F52L	0.794
4:86888185:A:T	F52L	0.794
4:86888187:A:G	F52L	0.794
4:86887782:C:G	R111T	0.790
4:86887857:A:G	L86P	0.750
4:86887880:T:A	E78D	0.738
4:86887880:T:G	E78D	0.738
4:86887868:T:A	E82D	0.735
4:86887868:T:G	E82D	0.735
4:86887848:A:G	L89P	0.729
4:86888263:C:A	W26C	0.707
4:86888263:C:G	W26C	0.707
4:86891477:A:G	L15S	0.703
4:86891501:C:G	R7T	0.699
4:86888236:C:A	W35C	0.689
4:86888236:C:G	W35C	0.689
4:86887881:T:A	E78V	0.688
4:86888235:A:G	S36P	0.675

dbSNP variants (sampled 300 via entrez): RS1000014182 (4:86884906 C>T), RS1000149523 (4:86884578 T>G), RS1000257291 (4:86885643 A>G), RS1000285040 (4:86899602 T>C), RS1000481767 (4:86879648 A>G), RS1000555445 (4:86886587 G>A), RS1000588403 (4:86886790 G>A), RS1000785209 (4:86880753 A>G), RS1000973001 (4:86894081 T>G), RS10011798 (4:86891411 G>A,C), RS1001230733 (4:86884065 A>C), RS1001237078 (4:86894348 T>C), RS10015121 (4:86892668 C>G), RS10015477 (4:86892900 G>A,T), RS10017360 (4:86898704 C>A,G,T)

Disease associations

OMIM: gene MIM:621278 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001958_16	Bulimia nervosa	4.000000e-06
GCST003476_4	Eyebrow thickness	2.000000e-06
GCST005580_91	Intraocular pressure	5.000000e-11
GCST005580_97	Intraocular pressure	7.000000e-11
GCST009467_2	Hemoglobin levels	4.000000e-06
GCST010243_98	Apolipoprotein B levels	3.000000e-10
GCST90002389_188	Lymphocyte percentage of white cells	2.000000e-10
GCST90002400_432	Plateletcrit	6.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0004509	hemoglobin measurement
EFO:0004615	apolipoprotein B measurement
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007985	platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	2
clothianidin	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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