C11orf42

Summary

C11orf42 (chromosome 11 open reading frame 42, HGNC:28541) is a protein-coding gene on chromosome 11p15.4, encoding Uncharacterized protein C11orf42 (Q8N5U0).

Located in sperm flagellum.

Source: NCBI Gene 160298 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_173525

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28541
Approved symbol	C11orf42
Name	chromosome 11 open reading frame 42
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Aliases	MGC34805
Ensembl gene	ENSG00000180878
Ensembl biotype	protein_coding
Entrez	160298

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000316375

RefSeq mRNA: 1 — MANE Select: NM_173525 NM_173525

CCDS: CCDS7759

Canonical transcript exons

ENST00000316375 — 3 exons

Exon	Start	End
ENSE00001255432	6209850	6210648
ENSE00001255442	6210912	6211135
ENSE00001255449	6205557	6205687

Expression profiles

Bgee: expression breadth ubiquitous, 146 present calls, max score 95.96.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0291 / max 27.5162, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
112836	0.0291	3

Top tissues by expression

242 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	95.96	gold quality
left testis	UBERON:0004533	84.15	gold quality
right testis	UBERON:0004534	82.92	gold quality
testis	UBERON:0000473	80.28	gold quality
cerebellar hemisphere	UBERON:0002245	64.86	gold quality
cerebellar cortex	UBERON:0002129	64.77	gold quality
right hemisphere of cerebellum	UBERON:0014890	64.60	gold quality
cerebellum	UBERON:0002037	63.26	gold quality
right uterine tube	UBERON:0001302	59.24	gold quality
rectum	UBERON:0001052	58.38	gold quality
apex of heart	UBERON:0002098	57.24	gold quality
mucosa of transverse colon	UBERON:0004991	57.15	gold quality
transverse colon	UBERON:0001157	56.92	gold quality
cortical plate	UBERON:0005343	55.65	gold quality
cartilage tissue	UBERON:0002418	54.23	gold quality
prefrontal cortex	UBERON:0000451	54.21	gold quality
colonic epithelium	UBERON:0000397	53.19	silver quality
small intestine Peyer’s patch	UBERON:0003454	52.90	gold quality
right lobe of liver	UBERON:0001114	52.88	gold quality
ganglionic eminence	UBERON:0004023	52.32	gold quality
small intestine	UBERON:0002108	52.28	gold quality
right lobe of thyroid gland	UBERON:0001119	51.57	gold quality
intestine	UBERON:0000160	50.41	gold quality
frontal cortex	UBERON:0001870	50.35	gold quality
colon	UBERON:0001155	50.20	gold quality
nasal cavity epithelium	UBERON:0005384	50.13	gold quality
large intestine	UBERON:0000059	49.96	gold quality
metanephros cortex	UBERON:0010533	49.88	gold quality
bone marrow cell	CL:0002092	49.75	gold quality
right frontal lobe	UBERON:0002810	49.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.31

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm5901	ENSMUSG00000078611
rattus_norvegicus	C1h11orf42	ENSRNOG00000071363

Protein

Protein identifiers

Uncharacterized protein C11orf42 — Q8N5U0 (reviewed: Q8N5U0)

All UniProt accessions (1): Q8N5U0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium. Flagellum.

RefSeq proteins (1): NP_775796* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031366	DUF4663	Family

Pfam: PF15668

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N5U0-F1	71.83	0.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): AML1_01, GOCC_MOTILE_CILIUM, OSF2_Q6, GOCC_CILIUM, GOCC_9PLUS2_MOTILE_CILIUM, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PAX3_TARGET_GENES, AML1_Q6, GSE2405_0H_VS_6H_A_PHAGOCYTOPHILUM_STIM_NEUTROPHIL_DN, GSE1566_WT_VS_EZH2_KO_LN_TCELL_UP, GSE22601_DOUBLE_NEGATIVE_VS_IMMATURE_CD4_SP_THYMOCYTE_DN, GSE22601_DOUBLE_NEGATIVE_VS_CD8_SINGLE_POSITIVE_THYMOCYTE_UP, chr11p15, CTGCAGY_UNKNOWN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (4): sperm flagellum (GO:0036126), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1
cellular anatomical structure	1

Protein interactions and networks

STRING

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf42	PDCL2	Q8N4E4	507
C11orf42	SPESP1	Q6UW49	447
C11orf42	C11orf16	Q9NQ32	447
C11orf42	GALNTL5	Q7Z4T8	417
C11orf42	C12orf56	Q8IXR9	397
C11orf42	DCAF4L1	Q3SXM0	324
C11orf42	C6orf136	Q5SQH8	305
C11orf42	SNX5	Q9Y5X3	302
C11orf42	TMEM217B	A0A494BZU4	299
C11orf42	TMEM217	Q8N7C4	297
C11orf42	TEX9	Q8N6V9	296
C11orf42	KIAA0930	Q6ICG6	273
C11orf42	ACTRT1	Q8TDG2	270
C11orf42	ZFAND4	Q86XD8	261
C11orf42	CAMTA1	Q9Y6Y1	255

IntAct

4 interactions, top by confidence:

A	B	Type	Score
C11orf42	SNX2	psi-mi:“MI:0914”(association)	0.530

BioGRID (7): SNX5 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX5 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX5 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), C11orf42 (Protein-peptide)

ESM2 similar proteins: A0MD28, A6YQT5, O12165, P03185, P05857, P05902, P05903, P06725, P07566, P08563, P08564, P0DJY0, P0DJZ9, P18139, P19725, P19811, P27959, P30118, P36343, P36551, P79209, P89439, P89457, Q04561, Q06502, Q1HVC3, Q3KSP4, Q3T0X9, Q642A4, Q6DFN5, Q6SW59, Q6X2U1, Q6X2U3, Q83017, Q8AZJ5, Q8B912, Q8CF25, Q8N5U0, Q8VA10, Q90932

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	4
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

415 predictions. Top by Δscore:

Variant	Effect	Δscore
11:6205684:TAAG:T	donor_loss	0.9900
11:6205687:GGTA:G	donor_loss	0.9900
11:6205685:AAGGT:A	donor_gain	0.9700
11:6205686:AGGT:A	donor_gain	0.9700
11:6205687:GGT:G	donor_gain	0.9600
11:6205682:GA:G	donor_gain	0.9500
11:6205688:G:GG	donor_gain	0.9500
11:6205689:T:A	donor_gain	0.9400
11:6205693:TA:T	donor_gain	0.9400
11:6205694:AA:A	donor_gain	0.9400
11:6205695:AA:A	donor_gain	0.9400
11:6205688:GT:G	donor_gain	0.9300
11:6210066:ACTCG:A	acceptor_gain	0.8900
11:6209837:T:A	acceptor_gain	0.8700
11:6209897:G:T	acceptor_gain	0.8700
11:6210285:T:TA	acceptor_gain	0.8700
11:6210066:ACTC:A	acceptor_gain	0.8600
11:6205684:TAAGG:T	donor_gain	0.8300
11:6205691:GGT:G	donor_loss	0.7900
11:6209661:CAGTA:C	acceptor_gain	0.7800
11:6209833:AAACT:A	acceptor_gain	0.7700
11:6209844:CTGCA:C	acceptor_loss	0.7700
11:6209845:TGCA:T	acceptor_loss	0.7700
11:6209846:GCAG:G	acceptor_loss	0.7700
11:6209847:CAGG:C	acceptor_loss	0.7700
11:6209849:G:C	acceptor_loss	0.7700
11:6210285:TGGC:T	acceptor_gain	0.7700
11:6209842:A:AG	acceptor_loss	0.7600
11:6205697:G:GG	donor_gain	0.7500
11:6205696:A:AG	donor_gain	0.7400

AlphaMissense

2107 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:6210360:T:C	F195L	0.995
11:6210362:C:A	F195L	0.995
11:6210362:C:G	F195L	0.995
11:6210376:T:C	F200S	0.994
11:6205667:T:A	W18R	0.993
11:6205667:T:C	W18R	0.993
11:6210361:T:C	F195S	0.992
11:6210375:T:C	F200L	0.992
11:6210377:T:A	F200L	0.992
11:6210377:T:G	F200L	0.992
11:6210259:T:A	V161D	0.991
11:6205669:G:C	W18C	0.988
11:6205669:G:T	W18C	0.988
11:6209892:T:C	F39L	0.985
11:6209894:C:A	F39L	0.985
11:6209894:C:G	F39L	0.985
11:6210273:T:C	F166L	0.982
11:6210275:C:A	F166L	0.982
11:6210275:C:G	F166L	0.982
11:6210361:T:G	F195C	0.982
11:6210358:C:A	A194D	0.981
11:6210183:T:C	F136L	0.977
11:6210185:C:A	F136L	0.977
11:6210185:C:G	F136L	0.977
11:6210355:T:A	V193D	0.977
11:6210376:T:G	F200C	0.977
11:6210450:T:A	W225R	0.975
11:6210450:T:C	W225R	0.975
11:6205681:G:C	K22N	0.972
11:6205681:G:T	K22N	0.972

dbSNP variants (sampled 300 via entrez): RS1000227170 (11:6207848 G>C), RS1000897187 (11:6209127 G>A,T), RS1001178256 (11:6209583 A>C), RS1002069171 (11:6203794 T>C), RS1002524945 (11:6203585 C>T), RS1002791588 (11:6211397 C>G), RS1002845365 (11:6211115 A>T), RS1002846722 (11:6205208 G>A), RS1003000198 (11:6211393 T>C), RS1003802540 (11:6207158 T>A,C,G), RS1004684916 (11:6209106 G>A), RS1005091766 (11:6209384 C>T), RS1005752913 (11:6206543 G>GC), RS1006345731 (11:6211424 C>G), RS1006636033 (11:6204723 G>C)

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

3 associations (top):

Study	Trait	p-value
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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