C9orf43

Summary

C9orf43 (chromosome 9 open reading frame 43, HGNC:23570) is a protein-coding gene on chromosome 9q32, encoding Uncharacterized protein C9orf43 (Q8TAL5).

At a glance

• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001278629

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23570
Approved symbol	C9orf43
Name	chromosome 9 open reading frame 43
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	MGC17358
Ensembl gene	ENSG00000157653
Ensembl biotype	protein_coding
Entrez	257169

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000288462, ENST00000374165, ENST00000490544, ENST00000940447, ENST00000940448

RefSeq mRNA: 3 — MANE Select: NM_001278629 NM_001278629, NM_001278630, NM_152786

CCDS: CCDS6796

Canonical transcript exons

ENST00000374165 — 14 exons

Exon	Start	End
ENSE00001091104	113428147	113428223
ENSE00001091107	113425643	113425730
ENSE00001091108	113425344	113425420
ENSE00001091109	113428900	113428963
ENSE00001091112	113424166	113424316
ENSE00001091115	113425019	113425076
ENSE00001204071	113423326	113423498
ENSE00001204075	113422549	113422585
ENSE00001204078	113421103	113421203
ENSE00001428650	113410747	113411001
ENSE00003562012	113413759	113413894
ENSE00003573252	113419108	113419165
ENSE00003663682	113413445	113413644
ENSE00003900986	113429172	113429690

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 92.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.2159 / max 117.7332, expressed in 1051 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98090	0.7657	414
98088	0.6293	354
98089	0.5301	280
98087	0.2092	60
98086	0.0599	7
98085	0.0218	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	92.84	gold quality
right testis	UBERON:0004534	91.59	gold quality
testis	UBERON:0000473	90.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.18	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.38	gold quality
sperm	CL:0000019	83.81	gold quality
adult organism	UBERON:0007023	77.10	gold quality
right adrenal gland	UBERON:0001233	67.73	gold quality
right adrenal gland cortex	UBERON:0035827	67.03	gold quality
islet of Langerhans	UBERON:0000006	65.93	gold quality
left adrenal gland	UBERON:0001234	65.73	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	65.70	gold quality
left adrenal gland cortex	UBERON:0035825	65.54	gold quality
bone marrow cell	CL:0002092	64.50	silver quality
adrenal cortex	UBERON:0001235	64.07	gold quality
right lobe of liver	UBERON:0001114	64.05	gold quality
adrenal gland	UBERON:0002369	62.76	gold quality
right uterine tube	UBERON:0001302	62.66	gold quality
bronchial epithelial cell	CL:0002328	60.98	silver quality
secondary oocyte	CL:0000655	60.36	silver quality
adenohypophysis	UBERON:0002196	60.35	gold quality
bronchus	UBERON:0002185	60.03	silver quality
pancreas	UBERON:0001264	59.59	gold quality
pituitary gland	UBERON:0000007	58.37	gold quality
bone marrow	UBERON:0002371	58.11	gold quality
cerebellar vermis	UBERON:0004720	57.83	gold quality
body of pancreas	UBERON:0001150	57.42	gold quality
left ovary	UBERON:0002119	57.07	gold quality
metanephros cortex	UBERON:0010533	56.49	gold quality
liver	UBERON:0002107	56.28	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-100618	no	144.24
E-ANND-3	no	3.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

12 targeting C9orf43, 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-4799-5P	99.82	70.60	2663
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-7854-3P	99.08	66.26	1117
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-938	97.41	68.28	656
HSA-MIR-6854-5P	96.77	65.96	848
HSA-MIR-4750-3P	96.65	64.38	512
HSA-MIR-6866-5P	96.64	68.06	624
HSA-MIR-4256	96.22	67.70	669
HSA-MIR-11181-5P	96.12	67.46	665

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4933430I17Rik	ENSMUSG00000058046
rattus_norvegicus	C5h9orf43	ENSRNOG00000024506

Protein

Protein identifiers

Uncharacterized protein C9orf43 — Q8TAL5 (reviewed: Q8TAL5)

All UniProt accessions (1): Q8TAL5

RefSeq proteins (3): NP_001265558, NP_001265559, NP_689999 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029134	DUF4647	Family

Pfam: PF15504

UniProt features (6 total): compositionally biased region 3, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAL5-F1	47.09	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): FOSTER_TOLERANT_MACROPHAGE_DN, DANG_BOUND_BY_MYC, MARSON_BOUND_BY_E2F4_UNSTIMULATED, BARX1_TARGET_GENES, DLX4_TARGET_GENES, DMRT1_TARGET_GENES, E2F2_TARGET_GENES, H1_6_TARGET_GENES, HSD17B8_TARGET_GENES, KAT5_TARGET_GENES, TEAD2_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF350_TARGET_GENES, ZNF407_TARGET_GENES, ZSCAN2_TARGET_GENES

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

234 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C9orf43	REDIC1	Q86WS4	671
C9orf43	FAM209A	Q5JX71	667
C9orf43	SPATA31G1	Q5VYM1	646
C9orf43	TMCO5A	Q8N6Q1	608
C9orf43	ZFAND4	Q86XD8	594
C9orf43	MAGEB16	A2A368	584
C9orf43	TULP2	O00295	575
C9orf43	PKDREJ	Q9NTG1	574
C9orf43	OR4X2	Q8NGF9	571
C9orf43	SPATA16	Q9BXB7	544
C9orf43	OR10A3	P58181	519
C9orf43	CATSPER1	Q8NEC5	510
C9orf43	OR7D2	Q96RA2	479
C9orf43	OR2AT4	A6NND4	451
C9orf43	WBP2NL	Q6ICG8	451

IntAct

12 interactions, top by confidence:

A	B	Type	Score
RABGAP1L	C9orf43	psi-mi:“MI:0915”(physical association)	0.570
C9orf43	ACTA2	psi-mi:“MI:0914”(association)	0.530
C9orf43	PARP1	psi-mi:“MI:0915”(physical association)	0.400
C9orf43	H1-5	psi-mi:“MI:0915”(physical association)	0.400
C9orf43	iglC2	psi-mi:“MI:0915”(physical association)	0.370
C9orf43	CFTR	psi-mi:“MI:0915”(physical association)	0.370
CFTR	C9orf43	psi-mi:“MI:0915”(physical association)	0.370
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): C9orf43 (Reconstituted Complex), C9orf43 (Two-hybrid), RABGAP1L (Affinity Capture-Luminescence), ACTA2 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), C9orf43 (Affinity Capture-MS), C9orf43 (Synthetic Lethality), C9orf43 (Proximity Label-MS), C9orf43 (Proximity Label-MS), ACTA2 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), C9orf43 (Affinity Capture-MS), C9orf43 (PCA), C9orf43 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GTH6, A0A1D5RMD1, A1KXM5, A2AEY4, A6NCI8, A6QQS3, A7KBS4, C4P6S0, O94713, P0C9Z7, P53963, P53976, Q0P670, Q0VAV2, Q10668, Q196W1, Q2KHR3, Q2YDJ5, Q32MG2, Q3V0A6, Q3V3Q4, Q4V8E9, Q5JRM2, Q68FV4, Q6AXV6, Q6AYN3, Q6NS59, Q7TSG5, Q80VJ6, Q80Y39, Q80YD3, Q810T2, Q86XD8, Q8C5U4, Q8CH19, Q8IWI9, Q8K4E0, Q8NDH2, Q8NEV8, Q8NFU7

Diamond homologs: Q8TAL5, Q95JN2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2081 predictions. Top by Δscore:

Variant	Effect	Δscore
9:113410054:C:CC	donor_gain	1.0000
9:113410054:CCAGG:C	donor_gain	1.0000
9:113410141:C:CC	acceptor_gain	1.0000
9:113410222:GCTCA:G	donor_loss	1.0000
9:113410224:TCA:T	donor_loss	1.0000
9:113410225:CACCG:C	donor_loss	1.0000
9:113410226:A:AC	donor_gain	1.0000
9:113410226:A:C	donor_loss	1.0000
9:113410227:C:CA	donor_loss	1.0000
9:113410227:C:CC	donor_gain	1.0000
9:113410227:CCG:C	donor_gain	1.0000
9:113410232:T:TA	donor_gain	1.0000
9:113419087:T:G	acceptor_gain	1.0000
9:113421101:A:AG	acceptor_gain	1.0000
9:113421102:G:GG	acceptor_gain	1.0000
9:113422536:T:A	acceptor_gain	1.0000
9:113422547:A:AG	acceptor_gain	1.0000
9:113422548:G:GA	acceptor_gain	1.0000
9:113422548:GCCA:G	acceptor_gain	1.0000
9:113422583:GTG:G	donor_gain	1.0000
9:113422586:GTGA:G	donor_loss	1.0000
9:113422587:T:A	donor_loss	1.0000
9:113422588:GAGT:G	donor_loss	1.0000
9:113423495:AGGA:A	donor_gain	1.0000
9:113423496:GGA:G	donor_gain	1.0000
9:113423496:GGAG:G	donor_gain	1.0000
9:113423497:GA:G	donor_gain	1.0000
9:113423497:GAG:G	donor_gain	1.0000
9:113423499:G:GG	donor_gain	1.0000
9:113424267:G:GG	donor_gain	1.0000

AlphaMissense

3058 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:113413568:G:C	W25C	0.986
9:113413568:G:T	W25C	0.986
9:113413548:T:C	C19R	0.979
9:113413563:T:C	C24R	0.978
9:113413581:C:A	R30S	0.978
9:113413582:G:C	R30P	0.976
9:113421172:T:A	W139R	0.973
9:113421172:T:C	W139R	0.973
9:113413563:T:A	C24S	0.972
9:113413564:G:C	C24S	0.972
9:113413565:C:G	C24W	0.972
9:113413518:T:A	W9R	0.970
9:113413518:T:C	W9R	0.970
9:113413556:C:A	H21Q	0.967
9:113413556:C:G	H21Q	0.967
9:113413566:T:A	W25R	0.967
9:113413566:T:C	W25R	0.967
9:113413520:G:C	W9C	0.965
9:113413520:G:T	W9C	0.965
9:113413533:T:C	C14R	0.965
9:113413550:T:G	C19W	0.964
9:113413579:G:C	R29P	0.961
9:113413548:T:A	C19S	0.959
9:113413549:G:C	C19S	0.959
9:113413549:G:A	C19Y	0.954
9:113413578:C:A	R29S	0.954
9:113413535:T:G	C14W	0.949
9:113413555:A:G	H21R	0.949
9:113413564:G:A	C24Y	0.945
9:113413533:T:A	C14S	0.942

dbSNP variants (sampled 300 via entrez): RS1000055043 (9:113425280 C>T), RS1000105441 (9:113425536 T>G), RS1000122171 (9:113418944 A>G), RS1000243342 (9:113419259 G>C), RS1000276581 (9:113411362 G>A,C), RS1000730909 (9:113417738 C>T), RS1000740138 (9:113424562 C>G), RS1001134182 (9:113421609 A>G), RS1001183313 (9:113424813 A>G), RS1001404581 (9:113414708 T>C,G), RS1001416823 (9:113421853 A>G), RS1001844529 (9:113410736 C>A,T), RS1001976031 (9:113416274 G>T), RS1002134939 (9:113422859 G>A), RS1002178653 (9:113412498 GAA>G)

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
jinfukang	increases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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