TTC17

Summary

TTC17 (tetratricopeptide repeat domain 17, HGNC:25596) is a protein-coding gene on chromosome 11p12-p11.2, encoding Tetratricopeptide repeat protein 17 (Q96AE7). Plays a role in primary ciliogenesis by modulating actin polymerization.

Involved in actin filament polymerization and cilium organization. Located in actin cytoskeleton; cytosol; and plasma membrane.

Source: NCBI Gene 55761 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 169 total
• MANE Select transcript: NM_018259

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25596
Approved symbol	TTC17
Name	tetratricopeptide repeat domain 17
Location	11p12-p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10890
Ensembl gene	ENSG00000052841
Ensembl biotype	protein_coding
OMIM	619388
Entrez	55761

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 18 protein_coding, 9 retained_intron, 1 non_stop_decay, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000039989, ENST00000299240, ENST00000418561, ENST00000524936, ENST00000525029, ENST00000525135, ENST00000525543, ENST00000526774, ENST00000529140, ENST00000530469, ENST00000530483, ENST00000533072, ENST00000533554, ENST00000534347, ENST00000534417, ENST00000703837, ENST00000867744, ENST00000867745, ENST00000867746, ENST00000867747, ENST00000867748, ENST00000867749, ENST00000867750, ENST00000929846, ENST00000929847, ENST00000969881, ENST00000969882, ENST00000969883, ENST00000969884, ENST00000969885

RefSeq mRNA: 6 — MANE Select: NM_018259 NM_001307943, NM_001376525, NM_001376526, NM_001376527, NM_001376528, NM_018259

CCDS: CCDS31466, CCDS76396, CCDS91461

Canonical transcript exons

ENST00000039989 — 24 exons

Exon	Start	End
ENSE00001100718	43396709	43396818
ENSE00001100723	43448002	43448122
ENSE00001100733	43391821	43391952
ENSE00001406712	43358920	43359113
ENSE00003459151	43444056	43444209
ENSE00003486651	43401446	43401558
ENSE00003493217	43405514	43405629
ENSE00003500545	43389652	43389821
ENSE00003516299	43397974	43398113
ENSE00003525028	43450082	43450241
ENSE00003526439	43405786	43405951
ENSE00003550105	43407138	43407215
ENSE00003555090	43490239	43490358
ENSE00003562161	43414590	43414776
ENSE00003567898	43403998	43404144
ENSE00003642415	43391465	43391576
ENSE00003642775	43399888	43400048
ENSE00003647747	43379233	43379322
ENSE00003657145	43451182	43451265
ENSE00003660131	43443325	43443584
ENSE00003664619	43397347	43397491
ENSE00003667308	43492020	43492163
ENSE00003678633	43407353	43407577
ENSE00003990057	43493773	43494931

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 98.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4004 / max 68.7528, expressed in 1728 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113939	6.9093	1706
113940	0.4911	253

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.55	gold quality
body of pancreas	UBERON:0001150	97.97	gold quality
calcaneal tendon	UBERON:0003701	97.49	gold quality
left ovary	UBERON:0002119	97.38	gold quality
right ovary	UBERON:0002118	97.22	gold quality
left lobe of thyroid gland	UBERON:0001120	97.14	gold quality
right lobe of thyroid gland	UBERON:0001119	97.12	gold quality
thyroid gland	UBERON:0002046	96.76	gold quality
right lung	UBERON:0002167	96.36	gold quality
body of uterus	UBERON:0009853	96.29	gold quality
adrenal tissue	UBERON:0018303	96.29	gold quality
tibial nerve	UBERON:0001323	96.28	gold quality
fundus of stomach	UBERON:0001160	96.24	gold quality
endocervix	UBERON:0000458	96.17	gold quality
pancreas	UBERON:0001264	96.01	gold quality
minor salivary gland	UBERON:0001830	96.00	gold quality
pylorus	UBERON:0001166	95.98	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.91	gold quality
body of stomach	UBERON:0001161	95.88	gold quality
saliva-secreting gland	UBERON:0001044	95.75	gold quality
adenohypophysis	UBERON:0002196	95.70	gold quality
lower esophagus mucosa	UBERON:0035834	95.67	gold quality
cerebellar hemisphere	UBERON:0002245	95.61	gold quality
cerebellar cortex	UBERON:0002129	95.58	gold quality
stomach	UBERON:0000945	95.52	gold quality
mucosa of stomach	UBERON:0001199	95.51	gold quality
skin of abdomen	UBERON:0001416	95.50	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.48	gold quality
pituitary gland	UBERON:0000007	95.47	gold quality
ectocervix	UBERON:0012249	95.46	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.16

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

93 targeting TTC17, 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-5011-5P	100.00	83.46	5820
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699

Literature-anchored findings (GeneRIF, showing 2)

• TTC17 is localized along the secretory pathway and was found to interact with resident proteins of ER-Golgi membranes. (PMID:31488582)
• TTC17 is an endoplasmic reticulum resident TPR-containing adaptor protein. (PMID:37949225)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ttc17	ENSDARG00000044812
mus_musculus	Ttc17	ENSMUSG00000027194
rattus_norvegicus	Ttc17	ENSRNOG00000010495
drosophila_melanogaster	CG11436	FBGN0029713
caenorhabditis_elegans		WBGENE00020553

Protein

Protein identifiers

Tetratricopeptide repeat protein 17 — Q96AE7 (reviewed: Q96AE7)

All UniProt accessions (5): A0A075B7B2, A0A994J3X0, Q96AE7, E9PN79, H0Y6S0

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in primary ciliogenesis by modulating actin polymerization.

Subunit / interactions. Interacts with CATIP.

Subcellular location. Cytoplasm. Cell membrane. Cytoskeleton.

Tissue specificity. Expressed in germ cells as well as in somatic cells of the testis (at protein level).

Similarity. Belongs to the TTC17 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96AE7-1	1	yes
Q96AE7-2	2

RefSeq proteins (6): NP_001294872, NP_001363454, NP_001363455, NP_001363456, NP_001363457, NP_060729* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat
IPR052630	TTC17	Family

Pfam: PF13181

UniProt features (14 total): repeat 6, splice variant 3, sequence variant 2, chain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96AE7-F1	71.24	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): GCM_GSPT1, AAAYRNCTG_UNKNOWN, WANG_LMO4_TARGETS_DN, KOYAMA_SEMA3B_TARGETS_UP, GGAANCGGAANY_UNKNOWN, GOBP_CILIUM_ORGANIZATION, GOBP_ACTIN_FILAMENT_ORGANIZATION, IRF1_Q6, GCM_NUMA1, TGACATY_UNKNOWN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, AACTTT_UNKNOWN, GCM_NF2, E12_Q6, GOBP_CELL_PROJECTION_ORGANIZATION

GO Biological Process (4): actin filament polymerization (GO:0030041), cilium organization (GO:0044782), Golgi to plasma membrane transport (GO:0006893), cell projection organization (GO:0030030)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), actin cytoskeleton (GO:0015629), cytoskeleton (GO:0005856), membrane (GO:0016020), exomer complex (GO:0034044)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
actin polymerization or depolymerization	1
protein polymerization	1
organelle organization	1
plasma membrane bounded cell projection organization	1
post-Golgi vesicle-mediated transport	1
vesicle-mediated transport to the plasma membrane	1
cellular component organization	1
binding	1
intracellular anatomical structure	1
cytoplasm	1
membrane	1
cell periphery	1
cytoskeleton	1
intracellular membraneless organelle	1
Golgi apparatus	1
trans-Golgi network transport vesicle	1
protein-containing complex	1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC17	VSIG10	Q8N0Z9	517
TTC17	UBFD1	O14562	485
TTC17	MCOLN2	Q8IZK6	415
TTC17	FAM174A	Q8TBP5	412
TTC17	HEATR5B	Q9P2D3	411
TTC17	LYPLAL1	Q5VWZ2	403
TTC17	GLYATL3	Q5SZD4	402
TTC17	PPM1N	Q8N819	401
TTC17	LDLRAD3	Q86YD5	398
TTC17	SHQ1	Q6PI26	381
TTC17	SMIM3	Q9BZL3	376
TTC17	SNTN	A6NMZ2	366
TTC17	SLC39A6	Q13433	350
TTC17	DNAJC16	Q9Y2G8	348
TTC17	HNRNPH3	P31942	346

IntAct

129 interactions, top by confidence:

A	B	Type	Score
C1QTNF9	C1QTNF9B	psi-mi:“MI:0914”(association)	0.780
TNFSF13B	IPO8	psi-mi:“MI:0914”(association)	0.640
YWHAE	RGS12	psi-mi:“MI:0914”(association)	0.610
YWHAE	SRSF10	psi-mi:“MI:0914”(association)	0.560
GABRE	FZD6	psi-mi:“MI:0914”(association)	0.530
PLXDC2	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
MCOLN3	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
DEFA1	MANBA	psi-mi:“MI:0914”(association)	0.530
OS9	AGRN	psi-mi:“MI:0914”(association)	0.530
ZACN	GPAA1	psi-mi:“MI:0914”(association)	0.530
ADAM33	LRP5	psi-mi:“MI:0914”(association)	0.530
GABRD	ATF6	psi-mi:“MI:0914”(association)	0.530
ENPP7	TUBB3	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
GABRA3	HLA-C	psi-mi:“MI:0914”(association)	0.530
C1orf54	EXTL3	psi-mi:“MI:0914”(association)	0.530
FKBP2	TTC13	psi-mi:“MI:0914”(association)	0.530
GPIHBP1	ADAM10	psi-mi:“MI:0914”(association)	0.530
TRPC4AP	SMCHD1	psi-mi:“MI:0914”(association)	0.530
TTC17	H3-4	psi-mi:“MI:0915”(physical association)	0.400
Nrip3	ILVBL	psi-mi:“MI:0914”(association)	0.350
RAB5C	GCA	psi-mi:“MI:0914”(association)	0.350
EGLN3	FAM168B	psi-mi:“MI:0914”(association)	0.350
LRRTM1	TMEM223	psi-mi:“MI:0914”(association)	0.350

BioGRID (161): TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS), TTC17 (Affinity Capture-MS)

ESM2 similar proteins: A0A0F7YYX3, A0A0K8R726, A0A0K8RK34, A0A1L4BJ46, A0A5C1ZW08, A0A5C1ZXT8, A0A5C2A2T2, B5DEL3, B6DCK1, B6DCK9, B6DCL6, C0HKG1, C5DVG0, E2AX35, E9PVB5, G1CWH5, O70514, O76061, O88452, O97561, P0C8E8, P0C8L9, P0DN48, P17322, P18301, P42579, P52823, P58239, P58911, P85831, P86899, Q08629, Q14512, Q4R6V5, Q5RAT2, Q5Y4U3, Q62288, Q802A9, Q8BJ83, Q8GV50

Diamond homologs: B5DEL3, E7F211, E9PVB5, Q96AE7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 153 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Neutrophil degranulation	16	3.9×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	8	11.1×	5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	131
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3913 predictions. Top by Δscore:

Variant	Effect	Δscore
11:43379227:TTGCA:T	acceptor_loss	1.0000
11:43379228:TGCAG:T	acceptor_loss	1.0000
11:43379229:GCAG:G	acceptor_loss	1.0000
11:43379230:CAGGT:C	acceptor_loss	1.0000
11:43379232:G:GA	acceptor_loss	1.0000
11:43389649:CAGA:C	acceptor_loss	1.0000
11:43389650:A:AG	acceptor_gain	1.0000
11:43389650:A:T	acceptor_loss	1.0000
11:43389651:G:A	acceptor_loss	1.0000
11:43389651:G:GA	acceptor_gain	1.0000
11:43389651:GA:G	acceptor_gain	1.0000
11:43389651:GAA:G	acceptor_gain	1.0000
11:43389651:GAAA:G	acceptor_gain	1.0000
11:43389651:GAAAC:G	acceptor_gain	1.0000
11:43389818:TCAGG:T	donor_loss	1.0000
11:43389819:CAGGT:C	donor_loss	1.0000
11:43389820:AGGTA:A	donor_loss	1.0000
11:43389821:GGTA:G	donor_loss	1.0000
11:43389822:G:T	donor_loss	1.0000
11:43389823:T:A	donor_loss	1.0000
11:43391577:G:GG	donor_gain	1.0000
11:43391816:TTCA:T	acceptor_loss	1.0000
11:43391818:CA:C	acceptor_loss	1.0000
11:43391819:A:AT	acceptor_loss	1.0000
11:43391819:AG:A	acceptor_gain	1.0000
11:43391820:G:A	acceptor_gain	1.0000
11:43391820:GGGT:G	acceptor_gain	1.0000
11:43391949:GAAG:G	donor_gain	1.0000
11:43391954:T:G	donor_loss	1.0000
11:43397344:TAG:T	acceptor_loss	1.0000

AlphaMissense

7548 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:43359078:T:A	W42R	1.000
11:43359078:T:C	W42R	1.000
11:43389668:A:C	Q89P	1.000
11:43389680:T:A	I93K	1.000
11:43389694:G:C	D98H	1.000
11:43389695:A:C	D98A	1.000
11:43389742:T:A	C114S	1.000
11:43389742:T:C	C114R	1.000
11:43389743:G:A	C114Y	1.000
11:43389743:G:C	C114S	1.000
11:43389744:C:G	C114W	1.000
11:43396787:T:C	C248R	1.000
11:43397388:T:C	L272P	1.000
11:43397414:G:C	A281P	1.000
11:43397477:G:A	G302R	1.000
11:43397477:G:C	G302R	1.000
11:43397477:G:T	G302W	1.000
11:43397478:G:A	G302E	1.000
11:43397478:G:T	G302V	1.000
11:43397987:A:G	Y311C	1.000
11:43397995:T:C	S314P	1.000
11:43398068:T:A	V338D	1.000
11:43398073:T:A	C340S	1.000
11:43398073:T:C	C340R	1.000
11:43398074:G:A	C340Y	1.000
11:43398074:G:C	C340S	1.000
11:43398075:T:G	C340W	1.000
11:43398086:T:C	L344P	1.000
11:43398098:T:C	L348S	1.000
11:43398103:G:C	A350P	1.000

dbSNP variants (sampled 300 via entrez): RS1000012796 (11:43387004 A>C), RS1000050524 (11:43474047 T>C), RS1000059042 (11:43473557 C>G), RS1000098104 (11:43378383 C>G), RS1000146357 (11:43464665 A>T), RS1000148136 (11:43422996 G>A), RS1000162472 (11:43391135 A>G), RS1000185595 (11:43479493 T>A,C), RS1000185844 (11:43471009 G>A), RS1000211208 (11:43378520 G>A), RS1000217210 (11:43437045 C>CA), RS1000223045 (11:43428900 A>G), RS1000264458 (11:43420989 A>G), RS1000334945 (11:43460197 A>G), RS1000348873 (11:43441206 G>A)

Disease associations

OMIM: gene MIM:619388 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002644_2	Birth length	1.000000e-06
GCST003194_35	Fibrinogen levels	3.000000e-13
GCST004121_2	Fibrinogen levels	3.000000e-10
GCST004122_20	Fibrinogen levels	2.000000e-10
GCST010002_236	Refractive error	2.000000e-24

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006784	body height at birth

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	7
Benzo(a)pyrene	affects methylation, increases expression	4
sodium arsenite	decreases expression, increases expression	3
bisphenol A	decreases expression, decreases methylation, affects cotreatment	2
Acetaminophen	decreases expression, increases expression	2
Cyclosporine	affects expression, decreases methylation	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
methylparaben	increases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
NSC 689534	affects binding, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Copper	affects binding, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1

Clinical trials (associated diseases)

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