SNTN

Summary

SNTN (sentan, cilia apical structure protein, HGNC:33706) is a protein-coding gene on chromosome 3p14.2, encoding Sentan (A6NMZ2). May be a component of the linker structure that bridges the ciliary membrane and peripheral singlet microtubules.

Predicted to enable calcium ion binding activity and calcium-dependent protein binding activity. Predicted to be located in cilium.

Source: NCBI Gene 132203 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001080537

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33706
Approved symbol	SNTN
Name	sentan, cilia apical structure protein
Location	3p14.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44379, S100AL
Ensembl gene	ENSG00000188817
Ensembl biotype	protein_coding
OMIM	617832
Entrez	132203

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000343837, ENST00000469440, ENST00000496807

RefSeq mRNA: 2 — MANE Select: NM_001080537 NM_001080537, NM_001348756

CCDS: CCDS33779

Canonical transcript exons

ENST00000343837 — 4 exons

Exon	Start	End
ENSE00001378139	63659725	63659864
ENSE00001379575	63654762	63654796
ENSE00001386013	63663937	63665212
ENSE00001387635	63652675	63652797

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 99.86.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2561 / max 108.4649, expressed in 25 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37138	0.1093	19
37139	0.0905	17
37140	0.0562	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.86	gold quality
bronchus	UBERON:0002185	99.69	gold quality
right uterine tube	UBERON:0001302	99.29	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	98.17	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.87	gold quality
oviduct epithelium	UBERON:0004804	97.45	gold quality
trachea	UBERON:0003126	95.12	gold quality
nasal cavity epithelium	UBERON:0005384	94.93	gold quality
epithelium of nasopharynx	UBERON:0001951	91.69	gold quality
fallopian tube	UBERON:0003889	90.91	gold quality
caput epididymis	UBERON:0004358	89.46	gold quality
left lobe of thyroid gland	UBERON:0001120	87.12	gold quality
right lobe of thyroid gland	UBERON:0001119	85.73	gold quality
nasal cavity mucosa	UBERON:0001826	83.80	gold quality
buccal mucosa cell	CL:0002336	83.53	silver quality
thyroid gland	UBERON:0002046	82.56	gold quality
right lung	UBERON:0002167	80.28	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.68	gold quality
lower lobe of lung	UBERON:0008949	71.41	silver quality
endometrium	UBERON:0001295	69.47	gold quality
left uterine tube	UBERON:0001303	69.34	gold quality
lung	UBERON:0002048	65.77	gold quality
upper lobe of lung	UBERON:0008948	61.18	gold quality
upper lobe of left lung	UBERON:0008952	60.51	gold quality
adult organism	UBERON:0007023	59.60	gold quality
endocervix	UBERON:0000458	59.49	gold quality
ileal mucosa	UBERON:0000331	57.93	silver quality
mucosa of transverse colon	UBERON:0004991	55.78	gold quality
sural nerve	UBERON:0015488	54.96	silver quality
tibialis anterior	UBERON:0001385	54.68	silver quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	2491.26
E-MTAB-10283	yes	1377.21
E-CURD-114	yes	1316.96
E-HCAD-1	yes	32.30
E-MTAB-10287	yes	27.17
E-GEOD-130148	yes	17.51
E-MTAB-7303	no	5.21
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting SNTN, 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-3163	100.00	77.23	8605
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
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
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-5697	99.39	67.74	1249

Literature-anchored findings (GeneRIF, showing 1)

• Data suggest that sentan is the first molecular component of the ciliary tip to bridge the cell membrane and peripheral singlet microtubules, making the distal portion of the cilia narrow and stiff to allow for better airway clearance or ovum transport. (PMID:18829862)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sntn	ENSMUSG00000044772
rattus_norvegicus	Sntn	ENSRNOG00000027383

Paralogs (21): CRNN (ENSG00000143536), S100A8 (ENSG00000143546), S100A7 (ENSG00000143556), S100B (ENSG00000160307), S100A1 (ENSG00000160678), S100A11 (ENSG00000163191), S100A9 (ENSG00000163220), S100A12 (ENSG00000163221), S100P (ENSG00000163993), S100G (ENSG00000169906), S100Z (ENSG00000171643), S100A7A (ENSG00000184330), S100A3 (ENSG00000188015), S100A16 (ENSG00000188643), S100A13 (ENSG00000189171), S100A14 (ENSG00000189334), S100A4 (ENSG00000196154), S100A5 (ENSG00000196420), S100A2 (ENSG00000196754), S100A10 (ENSG00000197747), S100A6 (ENSG00000197956)

Protein

Protein identifiers

Sentan — A6NMZ2 (reviewed: A6NMZ2)

Alternative names: Protein S100-A1-like, S100 calcium-binding protein A1-like

All UniProt accessions (3): A6NMZ2, C9JRU3, C9JXY5

UniProt curated annotations — full annotation on UniProt →

Function. May be a component of the linker structure that bridges the ciliary membrane and peripheral singlet microtubules.

Subcellular location. Cell projection. Cilium.

Miscellaneous. ‘Sentan’ means ’tip’ in Japanese.

Similarity. Belongs to the S-100 family.

RefSeq proteins (2): NP_001074006, NP_001335685 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR013787	S100_Ca-bd_sub	Domain
IPR034325	S-100_dom	Domain

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NMZ2-F1	81.85	0.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, chr3p14, GOCC_CILIUM, GOMF_CALCIUM_DEPENDENT_PROTEIN_BINDING, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIR9983_3P, MIR4261, MIR129_5P, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR147B_5P, MIR6074, MIR6509_5P, MIR382_3P, MIR573

GO Biological Process (0):

GO Molecular Function (3): calcium ion binding (GO:0005509), transition metal ion binding (GO:0046914), calcium-dependent protein binding (GO:0048306)

GO Cellular Component (2): cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metal ion binding	2
calcium ion binding	1
protein binding	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cellular anatomical structure	1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNTN	LDLRAD1	Q5T700	543
SNTN	FOXJ1	Q92949	518
SNTN	SHISA8	B8ZZ34	517
SNTN	TEKT1	Q969V4	503
SNTN	LINC03043	A4D0Y5	479
SNTN	DNAI1	Q9UI46	461
SNTN	DRC2	Q8IXS2	450
SNTN	CFAP58	Q5T655	435
SNTN	TMEM212	A6NML5	407
SNTN	DNAI2	Q9GZS0	407
SNTN	DNAH5	Q8TE73	401
SNTN	VSIG10	Q8N0Z9	401
SNTN	FAM174A	Q8TBP5	400
SNTN	FAM216B	Q8N7L0	395
SNTN	CIMAP3	Q8TCI5	394

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0JMA8, A0JPI4, A1A535, A1A5P5, A6NMZ2, B7FF67, P34550, Q06A97, Q0P561, Q14156, Q14D04, Q2TAA8, Q3HRN7, Q3HRN8, Q3HRP1, Q3HRP5, Q3MHP3, Q5PPU5, Q5PQS3, Q5QIT3, Q5SPP5, Q5SY68, Q5THR3, Q641A2, Q6R556, Q6ZQ18, Q75LU8, Q7FRS8, Q7Z3E5, Q8BG67, Q8BMD7, Q8C9X1, Q8IGJ0, Q8LAS7, Q8LEM7, Q8NHS4, Q8VZQ4, Q8W475, Q91WD9, Q99P25

Diamond homologs: A6NMZ2, B7FF67, P29034, P35467, Q0P561, Q503K9, Q7LZT1, Q8C9X1, P02639, P23297, P56565, Q5RC36, O77691, P02632, P02633, P02634, P02638, P04163, P04271, P04631, P05942, P05943, P05964, P06702, P06703, P07091, P08207, P10462, P14069, P24479, P24480, P25815, P26447, P27003, P27005, P28318, P28783, P29377, P30801, P31725

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

596 predictions. Top by Δscore:

Variant	Effect	Δscore
3:63653979:A:AG	donor_gain	0.9900
3:63653979:A:G	donor_gain	0.9900
3:63652794:AAAGG:A	donor_loss	0.9800
3:63652795:AAGG:A	donor_loss	0.9800
3:63652797:GGTC:G	donor_loss	0.9800
3:63652798:G:GA	donor_loss	0.9800
3:63652799:T:A	donor_loss	0.9700
3:63663931:TCACA:T	acceptor_loss	0.9400
3:63663932:CACA:C	acceptor_loss	0.9400
3:63663935:A:AT	acceptor_loss	0.9400
3:63663936:G:GA	acceptor_loss	0.9400
3:63663674:T:A	acceptor_gain	0.9200
3:63663920:T:G	acceptor_loss	0.9000
3:63663782:GAATT:G	donor_gain	0.8900
3:63663787:G:GG	donor_gain	0.8800
3:63663935:AG:A	acceptor_gain	0.8800
3:63663936:GG:G	acceptor_gain	0.8800
3:63652798:G:GG	donor_gain	0.8700
3:63659723:A:AG	acceptor_gain	0.8500
3:63659724:G:GG	acceptor_gain	0.8500
3:63654792:GAAAG:G	donor_loss	0.8400
3:63654793:AAAGG:A	donor_loss	0.8400
3:63654794:AAGGT:A	donor_loss	0.8400
3:63654795:AGGTA:A	donor_loss	0.8400
3:63654796:GGTAA:G	donor_loss	0.8400
3:63654797:G:GA	donor_loss	0.8400
3:63654798:T:C	donor_loss	0.8400
3:63654799:A:AG	donor_loss	0.8400
3:63654757:GGC:G	donor_loss	0.8300
3:63654758:GCA:G	donor_loss	0.8300

AlphaMissense

970 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:63659778:T:C	F67L	0.956
3:63659780:C:A	F67L	0.956
3:63659780:C:G	F67L	0.956
3:63659856:T:C	F93L	0.938
3:63659858:C:A	F93L	0.938
3:63659858:C:G	F93L	0.938
3:63664018:T:C	F123L	0.934
3:63664020:C:A	F123L	0.934
3:63664020:C:G	F123L	0.934
3:63659833:T:C	L85P	0.933
3:63659750:A:C	E57D	0.924
3:63659750:A:T	E57D	0.924
3:63659754:G:C	A59P	0.899
3:63659749:A:T	E57V	0.895
3:63659769:G:C	A64P	0.891
3:63659847:T:C	F90L	0.888
3:63659849:T:A	F90L	0.888
3:63659849:T:G	F90L	0.888
3:63659761:C:A	A61D	0.886
3:63659779:T:C	F67S	0.878
3:63659760:G:C	A61P	0.875
3:63664019:T:C	F123S	0.872
3:63659848:T:C	F90S	0.869
3:63664036:A:C	S129R	0.864
3:63664038:C:A	S129R	0.864
3:63664038:C:G	S129R	0.864
3:63659824:C:A	A82D	0.860
3:63664009:T:C	F120L	0.860
3:63664011:T:A	F120L	0.860
3:63664011:T:G	F120L	0.860

dbSNP variants (sampled 300 via entrez): RS1000565770 (3:63664357 A>T), RS1000938275 (3:63653105 A>T), RS1001105066 (3:63655531 C>A), RS1001111468 (3:63662390 C>A,T), RS1001516341 (3:63657404 A>G,T), RS1001612478 (3:63651344 TAA>T,TA,TAAA), RS1001702521 (3:63653440 G>A), RS1001733545 (3:63653179 T>C), RS1001799305 (3:63658837 G>A), RS1001958260 (3:63663521 A>G,T), RS1002113827 (3:63663874 T>A), RS1002168117 (3:63659058 G>A,T), RS1002558572 (3:63658379 G>A), RS1002608695 (3:63652310 C>T), RS1002628176 (3:63655946 T>C)

Disease associations

OMIM: gene MIM:617832 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003854_29	Gut microbiota (functional units)	1.000000e-08
GCST006138_41	Resting-state electroencephalogram vigilance	2.000000e-06
GCST008097_20	Bisphosphonate-associated atypical femoral fracture	6.000000e-08
GCST008506_7	Stress sensitivity (neuroticism score x major depressive disorder status interaction)	8.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007874	gut microbiome measurement
EFO:0004357	electroencephalogram measurement
EFO:0009958	response to bisphosphonate
EFO:0009960	atypical femoral fracture
EFO:0007660	neuroticism measurement

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
Tobacco Smoke Pollution	affects expression, decreases expression	2
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Smoke	increases abundance, increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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