C11orf58

Summary

C11orf58 (chromosome 11 open reading frame 58, HGNC:16990) is a protein-coding gene on chromosome 11p15.2, encoding Small acidic protein (O00193).

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_014267

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16990
Approved symbol	C11orf58
Name	chromosome 11 open reading frame 58
Location	11p15.2
Locus type	gene with protein product
Status	Approved
Aliases	SMAP, Hero20
Ensembl gene	ENSG00000110696
Ensembl biotype	protein_coding
OMIM	619625
Entrez	10944

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 16 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000228136, ENST00000524439, ENST00000524461, ENST00000524508, ENST00000525106, ENST00000525256, ENST00000525684, ENST00000527893, ENST00000528634, ENST00000531658, ENST00000908021, ENST00000908022, ENST00000908023, ENST00000917286, ENST00000917287, ENST00000917288, ENST00000917289, ENST00000917290, ENST00000917291, ENST00000917292, ENST00000917293, ENST00000971722

RefSeq mRNA: 1 — MANE Select: NM_014267 NM_014267

CCDS: CCDS7822

Canonical transcript exons

ENST00000228136 — 5 exons

Exon	Start	End
ENSE00000704186	16748097	16748157
ENSE00002190925	16754871	16758340
ENSE00002249891	16738647	16738841
ENSE00003607343	16752785	16752894
ENSE00003641634	16744601	16744684

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 99.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 162.8919 / max 1794.9435, expressed in 1827 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113245	162.0979	1827
113246	0.7940	445

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	99.60	gold quality
ganglionic eminence	UBERON:0004023	98.94	gold quality
embryo	UBERON:0000922	98.93	gold quality
islet of Langerhans	UBERON:0000006	98.69	gold quality
tibialis anterior	UBERON:0001385	98.67	gold quality
monocyte	CL:0000576	98.61	gold quality
ventricular zone	UBERON:0003053	98.57	gold quality
leukocyte	CL:0000738	98.49	gold quality
gall bladder	UBERON:0002110	98.48	gold quality
vermiform appendix	UBERON:0001154	98.45	gold quality
smooth muscle tissue	UBERON:0001135	98.37	gold quality
endothelial cell	CL:0000115	98.33	gold quality
stromal cell of endometrium	CL:0002255	98.30	gold quality
popliteal artery	UBERON:0002250	98.27	gold quality
tibial artery	UBERON:0007610	98.27	gold quality
left ovary	UBERON:0002119	98.24	gold quality
cortical plate	UBERON:0005343	98.17	gold quality
descending thoracic aorta	UBERON:0002345	98.16	gold quality
right coronary artery	UBERON:0001625	98.12	gold quality
deltoid	UBERON:0001476	98.09	gold quality
epithelial cell of pancreas	CL:0000083	98.07	gold quality
aorta	UBERON:0000947	98.04	gold quality
left coronary artery	UBERON:0001626	98.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.91	gold quality
right ovary	UBERON:0002118	97.89	gold quality
right lung	UBERON:0002167	97.88	gold quality
left ventricle myocardium	UBERON:0006566	97.87	gold quality
thoracic aorta	UBERON:0001515	97.86	gold quality
body of uterus	UBERON:0009853	97.86	gold quality
ascending aorta	UBERON:0001496	97.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

195 targeting C11orf58, 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-9-5P	100.00	72.28	2361
HSA-MIR-98-3P	100.00	74.08	3907
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:56106	ENSDARG00000022564
mus_musculus	1110004F10Rik	ENSMUSG00000030663
rattus_norvegicus	C1h11orf58	ENSRNOG00000053659

Protein

Protein identifiers

Small acidic protein — O00193 (reviewed: O00193)

All UniProt accessions (4): O00193, E9PM92, E9PQA1, E9PRZ9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SMAP family.

RefSeq proteins (1): NP_055082* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026714	SMAP	Family
IPR028124	SMAP_dom	Domain

Pfam: PF15477

UniProt features (16 total): modified residue 8, cross-link 3, compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00193-F1	66.15	0.10

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (11): 147, 174, 179, 13, 62, 75, 15, 17, 63, 87, 127

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): HORIUCHI_WTAP_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, BASAKI_YBX1_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN, BLALOCK_ALZHEIMERS_DISEASE_DN, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN, DELPUECH_FOXO3_TARGETS_UP, SHEN_SMARCA2_TARGETS_UP

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (1): cellular_component (GO:0005575)

Protein interactions and networks

STRING

854 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C11orf58	CALM1	P02593	567
C11orf58	CALML3	P27482	523
C11orf58	CALML6	Q8TD86	523
C11orf58	CALML4	Q96GE6	523
C11orf58	CALML5	Q9NZT1	523
C11orf58	BRCA2	P51587	486
C11orf58	VTN	P01141	466
C11orf58	SEM1	Q6ZVN7	448
C11orf58	FXN	Q16595	418
C11orf58	THRSP	Q92748	401
C11orf58	APOH	P02749	397
C11orf58	NFS1	Q9Y697	397
C11orf58	ISCU	Q9H1K1	392
C11orf58	LYRM4	Q9HD34	378
C11orf58	PTMA	P06454	366

IntAct

45 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
A2M	SMAP	psi-mi:“MI:0915”(physical association)	0.550
EEF1G	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SMAP	FBN3	psi-mi:“MI:0915”(physical association)	0.370
CEP126	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SMAP	MBTPS1	psi-mi:“MI:0915”(physical association)	0.370
POLR2C	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SMAP	PTN	psi-mi:“MI:0915”(physical association)	0.370
SMAP	RNF19A	psi-mi:“MI:0915”(physical association)	0.370
RPLP1	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SEMA5B	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SF3B1	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SHC1	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SMAP	SLC44A1	psi-mi:“MI:0915”(physical association)	0.370
SMAP	SNCAIP	psi-mi:“MI:0915”(physical association)	0.370
TRA2A	SMAP	psi-mi:“MI:0915”(physical association)	0.370
SMAP	ZBTB48	psi-mi:“MI:0915”(physical association)	0.370
SLX4	SMAP	psi-mi:“MI:0914”(association)	0.350
MARK2	SMAP	psi-mi:“MI:0914”(association)	0.350
WDR48	UNC13B	psi-mi:“MI:0914”(association)	0.350
BMX	SMAP	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
KLHDC3	SMAP	psi-mi:“MI:0914”(association)	0.350
SYT2	SMAP	psi-mi:“MI:0914”(association)	0.350
MFSD14A	FAM171A2	psi-mi:“MI:0914”(association)	0.350
	MYO1C	psi-mi:“MI:0914”(association)	0.350
PA	SMAP	psi-mi:“MI:0914”(association)	0.350

BioGRID (101): C11orf58 (Co-fractionation), C11orf58 (Co-fractionation), HMGN5 (Co-fractionation), HYPK (Co-fractionation), NAP1L1 (Co-fractionation), PTMA (Co-fractionation), C11orf58 (Proximity Label-MS), C11orf58 (Affinity Capture-MS), C11orf58 (Proximity Label-MS), C11orf58 (Affinity Capture-MS), C11orf58 (Proximity Label-MS), C11orf58 (Affinity Capture-MS), C11orf58 (Affinity Capture-RNA), C11orf58 (Proximity Label-MS), C11orf58 (Proximity Label-MS)

ESM2 similar proteins: A2AQ19, B5XE27, O00193, O43768, O88271, P60840, P60841, P68210, P68211, Q0IIX4, Q28GU6, Q3MHJ0, Q3MHL8, Q3T062, Q4ADK4, Q4ADK7, Q5M947, Q5RAD5, Q5RD18, Q5RKH3, Q5U2T8, Q5ZIF8, Q5ZIH9, Q5ZJ97, Q6DDU5, Q6DEB4, Q6GQG3, Q6NVR1, Q6PII3, Q75QI0, Q75UQ2, Q7TN31, Q7ZVC9, Q7ZXH9, Q8HXY9, Q8K039, Q8NDD1, Q90368, Q91WE2, Q92541

Diamond homologs: O00193, Q0IIX4, Q3MHL8, Q5RD18, Q6DDU5, Q7ZVC9, Q90368, Q9I9J6, Q9R0P4, A5D7J3, Q1ED39, Q9Z2Q2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

9 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

1405 predictions. Top by Δscore:

Variant	Effect	Δscore
11:16754869:A:AG	acceptor_gain	1.0000
11:16754870:G:GG	acceptor_gain	1.0000
11:16754870:GGTA:G	acceptor_gain	1.0000
11:16738778:G:GT	donor_gain	0.9900
11:16738779:A:G	donor_gain	0.9900
11:16738869:GGT:G	donor_gain	0.9900
11:16743381:G:GG	donor_gain	0.9900
11:16743384:A:T	donor_gain	0.9900
11:16744599:AGCT:A	acceptor_gain	0.9900
11:16744599:AGCTG:A	acceptor_gain	0.9900
11:16744600:GCT:G	acceptor_gain	0.9900
11:16744600:GCTG:G	acceptor_gain	0.9900
11:16744600:GCTGG:G	acceptor_gain	0.9900
11:16752890:G:GG	donor_gain	0.9900
11:16754037:T:G	donor_gain	0.9900
11:16754863:T:A	acceptor_gain	0.9900
11:16754869:AG:A	acceptor_gain	0.9900
11:16754870:GG:G	acceptor_gain	0.9900
11:16754870:GGT:G	acceptor_gain	0.9900
11:16738839:G:GT	donor_gain	0.9800
11:16738839:GAT:G	donor_gain	0.9800
11:16738842:G:GG	donor_gain	0.9800
11:16743387:G:GG	donor_gain	0.9800
11:16744599:A:AG	acceptor_gain	0.9800
11:16744600:G:GG	acceptor_gain	0.9800
11:16744681:AAAG:A	donor_loss	0.9800
11:16744682:AAGGT:A	donor_loss	0.9800
11:16744683:AGG:A	donor_loss	0.9800
11:16744684:GG:G	donor_loss	0.9800
11:16744685:GTA:G	donor_loss	0.9800

AlphaMissense

1226 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:16744616:T:A	W27R	1.000
11:16744616:T:C	W27R	1.000
11:16744618:G:C	W27C	1.000
11:16744618:G:T	W27C	1.000
11:16744632:T:C	L32S	1.000
11:16744658:T:C	F41L	1.000
11:16744659:T:C	F41S	1.000
11:16744659:T:G	F41C	1.000
11:16744660:C:A	F41L	1.000
11:16744660:C:G	F41L	1.000
11:16744665:G:C	R43T	1.000
11:16744666:A:C	R43S	1.000
11:16744666:A:T	R43S	1.000
11:16744668:T:A	L44H	1.000
11:16744668:T:C	L44P	1.000
11:16744671:T:C	M45T	1.000
11:16744673:G:A	G46S	1.000
11:16744673:G:C	G46R	1.000
11:16744673:G:T	G46C	1.000
11:16744674:G:A	G46D	1.000
11:16744674:G:T	G46V	1.000
11:16748109:G:C	G54R	1.000
11:16748110:G:A	G54D	1.000
11:16748122:T:A	I58K	1.000
11:16748124:G:A	G59R	1.000
11:16748124:G:C	G59R	1.000
11:16748125:G:A	G59E	1.000
11:16752815:T:A	L80Q	1.000
11:16752815:T:C	L80P	1.000
11:16752871:C:G	H99D	1.000

dbSNP variants (sampled 300 via entrez): RS1000432503 (11:16739699 A>G), RS1000486362 (11:16739508 G>A), RS1000487117 (11:16751640 TG>T), RS1000550096 (11:16747568 T>A), RS1000735703 (11:16746735 C>T), RS1000749592 (11:16747193 C>G,T), RS1000767335 (11:16738555 T>A,C,G), RS1000818392 (11:16738362 G>C), RS1001021869 (11:16740431 C>G,T), RS1001051549 (11:16740608 G>T), RS1001623192 (11:16740217 G>A,T), RS1001725531 (11:16752547 A>G), RS1001779233 (11:16745774 C>T), RS1001871379 (11:16745202 G>A), RS1001958236 (11:16739108 T>G)

Disease associations

OMIM: gene MIM:619625 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST004602_192	Mean corpuscular volume	5.000000e-18
GCST004611_177	High light scatter reticulocyte count	2.000000e-12
GCST004612_115	High light scatter reticulocyte percentage of red cells	7.000000e-15
GCST004622_34	Reticulocyte count	6.000000e-19
GCST004630_246	Mean corpuscular hemoglobin	1.000000e-18
GCST005795_32	Femoral neck bone mineral density	3.000000e-10
GCST005796_18	Lumbar spine bone mineral density	6.000000e-10
GCST006288_117	Heel bone mineral density	2.000000e-07
GCST006288_32	Heel bone mineral density	1.000000e-18
GCST006288_727	Heel bone mineral density	2.000000e-11
GCST006979_780	Heel bone mineral density	6.000000e-14
GCST007576_52	Chronotype	7.000000e-12
GCST010866_78	Coronary artery disease	2.000000e-09
GCST90002385_198	High light scatter reticulocyte count	1.000000e-14
GCST90002386_348	High light scatter reticulocyte percentage of red cells	8.000000e-19
GCST90002397_517	Mean spheric corpuscular volume	3.000000e-18
GCST90002403_245	Red blood cell count	4.000000e-13
GCST90002405_277	Reticulocyte count	5.000000e-21
GCST90002406_365	Reticulocyte fraction of red cells	1.000000e-27
GCST90011900_64	Serum alkaline phosphatase levels	2.000000e-11

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0007785	femoral neck bone mineral density
EFO:0007701	spine bone mineral density
EFO:0009270	heel bone mineral density
EFO:0008328	chronotype measurement
EFO:0004305	erythrocyte count
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Ozone	increases oxidation, affects expression, increases abundance, affects cotreatment	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases oxidation	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Carbamazepine	affects expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Lead	affects expression	1
Valproic Acid	affects expression	1
Cyclosporine	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1LP	Abcam HeLa C11orf58 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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