TTC13

Summary

TTC13 (tetratricopeptide repeat domain 13, HGNC:26204) is a protein-coding gene on chromosome 1q42.2, encoding Tetratricopeptide repeat protein 13 (Q8NBP0).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 127 total
• MANE Select transcript: NM_024525

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26204
Approved symbol	TTC13
Name	tetratricopeptide repeat domain 13
Location	1q42.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22584
Ensembl gene	ENSG00000143643
Ensembl biotype	protein_coding
Entrez	79573

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 25 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000366661, ENST00000366662, ENST00000466507, ENST00000471302, ENST00000481976, ENST00000486879, ENST00000519379, ENST00000522399, ENST00000522821, ENST00000902282, ENST00000902283, ENST00000902284, ENST00000902285, ENST00000902286, ENST00000902287, ENST00000902288, ENST00000902289, ENST00000902290, ENST00000902291, ENST00000931889, ENST00000931890, ENST00000944173, ENST00000944174, ENST00000944175, ENST00000944176, ENST00000944177, ENST00000944178, ENST00000944179, ENST00000944180

RefSeq mRNA: 10 — MANE Select: NM_024525 NM_001122835, NM_001376507, NM_001376508, NM_001376509, NM_001376510, NM_001376511, NM_001376512, NM_001376513, NM_001376514, NM_024525

CCDS: CCDS1588, CCDS44332

Canonical transcript exons

ENST00000366661 — 23 exons

Exon	Start	End
ENSE00000961350	230923841	230923933
ENSE00000961351	230921421	230921504
ENSE00000961353	230916193	230916302
ENSE00000961355	230911470	230911549
ENSE00000961356	230908942	230909020
ENSE00000961357	230908712	230908791
ENSE00001070040	230928937	230929093
ENSE00001070042	230925517	230925647
ENSE00001070043	230939386	230939496
ENSE00001070045	230931298	230931472
ENSE00001070048	230940440	230940556
ENSE00001205712	230924841	230924973
ENSE00001260652	230958224	230958299
ENSE00001260661	230961209	230961303
ENSE00001442271	230978560	230978861
ENSE00001948917	230906243	230907019
ENSE00003467797	230943806	230943898
ENSE00003546620	230920510	230920594
ENSE00003599394	230945389	230945454
ENSE00003652053	230954333	230954403
ENSE00003656777	230931736	230931877
ENSE00003679488	230933779	230933861
ENSE00003682159	230912623	230912758

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 93.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.4270 / max 193.3725, expressed in 1781 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17968	13.4270	1781

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	93.47	gold quality
rectum	UBERON:0001052	92.85	gold quality
monocyte	CL:0000576	92.07	gold quality
mononuclear cell	CL:0000842	91.99	gold quality
leukocyte	CL:0000738	91.64	gold quality
spleen	UBERON:0002106	89.55	gold quality
transverse colon	UBERON:0001157	88.60	gold quality
body of stomach	UBERON:0001161	88.32	gold quality
lymph node	UBERON:0000029	88.21	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.20	gold quality
body of pancreas	UBERON:0001150	88.01	gold quality
mucosa of transverse colon	UBERON:0004991	87.25	gold quality
blood	UBERON:0000178	87.03	gold quality
germinal epithelium of ovary	UBERON:0001304	87.00	gold quality
tibial nerve	UBERON:0001323	86.64	gold quality
stomach	UBERON:0000945	86.53	gold quality
vermiform appendix	UBERON:0001154	86.38	gold quality
right coronary artery	UBERON:0001625	86.13	gold quality
pancreas	UBERON:0001264	86.09	gold quality
small intestine	UBERON:0002108	85.85	gold quality
cortical plate	UBERON:0005343	85.54	gold quality
mucosa of stomach	UBERON:0001199	85.52	gold quality
upper lobe of left lung	UBERON:0008952	85.52	gold quality
right uterine tube	UBERON:0001302	85.49	gold quality
left coronary artery	UBERON:0001626	85.46	gold quality
calcaneal tendon	UBERON:0003701	85.23	gold quality
intestine	UBERON:0000160	85.18	gold quality
skin of hip	UBERON:0001554	85.10	gold quality
colon	UBERON:0001155	85.08	gold quality
ascending aorta	UBERON:0001496	85.03	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.58
E-MTAB-6058	no	109.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

80 targeting TTC13, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514

Literature-anchored findings (GeneRIF, showing 1)

• TTC13 expression and STAT3 activation may form a positive feedback loop to promote ccRCC progression. (PMID:37927783)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ttc13	ENSDARG00000063242
mus_musculus	Ttc13	ENSMUSG00000037300
rattus_norvegicus	Ttc13	ENSRNOG00000018884
drosophila_melanogaster	Tmtc4	FBGN0038324
caenorhabditis_elegans		WBGENE00021444

Paralogs (14): IFT88 (ENSG00000032742), TTC7A (ENSG00000068724), TMTC4 (ENSG00000125247), TMTC1 (ENSG00000133687), TMTC3 (ENSG00000139324), TTC6 (ENSG00000139865), BBS4 (ENSG00000140463), OGT (ENSG00000147162), CFAP70 (ENSG00000156042), TTC8 (ENSG00000165533), TTC7B (ENSG00000165914), TTC16 (ENSG00000167094), TMTC2 (ENSG00000179104), TTC34 (ENSG00000215912)

Protein

Protein identifiers

Tetratricopeptide repeat protein 13 — Q8NBP0 (reviewed: Q8NBP0)

All UniProt accessions (7): Q8NBP0, A0A384NPL4, E5RG15, E5RHB3, E5RJP6, H0YB10, H0YBV3

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NBP0-1	1	yes
Q8NBP0-2	2

RefSeq proteins (10): NP_001116307, NP_001363436, NP_001363437, NP_001363438, NP_001363439, NP_001363440, NP_001363441, NP_001363442, NP_001363443, NP_078801* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat

Pfam: PF00515, PF13181, PF13432

UniProt features (12 total): repeat 7, sequence conflict 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBP0-F1	84.34	0.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 154 (showing top): MYOGENIN_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, ATCATGA_MIR433, BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, KOYAMA_SEMA3B_TARGETS_DN, FARMER_BREAST_CANCER_APOCRINE_VS_BASAL, GSE5503_MLN_DC_VS_PLN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, ARID5B_TARGET_GENES, ARNT2_TARGET_GENES, DIDO1_TARGET_GENES, E2F2_TARGET_GENES, E2F5_TARGET_GENES, HOXC6_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

1404 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC13	OR4K15	Q8NH41	621
TTC13	TPGS1	Q6ZTW0	575
TTC13	CDC42EP5	Q6NZY7	519
TTC13	PABIR2	Q7Z309	474
TTC13	NXPH1	P58417	470
TTC13	RNF217	Q8TC41	461
TTC13	BTBD17	A6NE02	454
TTC13	UBR7	Q8N806	413
TTC13	SANBR	Q6NSI8	412
TTC13	TTC32	Q5I0X7	403
TTC13	TTC31	Q49AM3	399
TTC13	RNF19B	Q6ZMZ0	397
TTC13	NOL12	Q9UGY1	386
TTC13	TTC14	Q96N46	355
TTC13	E7EVR1	E7EVR1	340

IntAct

71 interactions, top by confidence:

A	B	Type	Score
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
DEFA1	MANBA	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
	HAX1	psi-mi:“MI:0914”(association)	0.350
EGLN3	FAM168B	psi-mi:“MI:0914”(association)	0.350
M	NPEPPSL1	psi-mi:“MI:0914”(association)	0.350
M2	IPO5	psi-mi:“MI:0914”(association)	0.350
M2	AGPS	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
	PLOD2	psi-mi:“MI:0914”(association)	0.350
IGF1R	HAX1	psi-mi:“MI:0914”(association)	0.350
INSR	HAX1	psi-mi:“MI:0914”(association)	0.350
CANX	HLA-A	psi-mi:“MI:0914”(association)	0.350
CCDC47	ESYT2	psi-mi:“MI:0914”(association)	0.350
TMEM106A	QSOX1	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CSTL1	DENND11	psi-mi:“MI:0914”(association)	0.350
TMEM106A	RTL8C	psi-mi:“MI:0914”(association)	0.350
FKBP2	HLA-DQA1	psi-mi:“MI:0914”(association)	0.350
GRAMD1B	ADD2	psi-mi:“MI:0914”(association)	0.350
TMEM106A	TMEM131L	psi-mi:“MI:0914”(association)	0.350
HLA-G	TMEM131L	psi-mi:“MI:0914”(association)	0.350
BTNL2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM131L	psi-mi:“MI:0914”(association)	0.350
BRICD5	TMEM131L	psi-mi:“MI:0914”(association)	0.350
LY86	TMEM131L	psi-mi:“MI:0914”(association)	0.350

BioGRID (106): TTC13 (Proximity Label-MS), TTC13 (Affinity Capture-MS), TTC13 (Affinity Capture-MS), TTC13 (Synthetic Lethality), TTC13 (Affinity Capture-MS), TTC13 (Affinity Capture-MS), TTC13 (Affinity Capture-MS), TTC13 (Proximity Label-MS), TTC13 (Proximity Label-MS), TTC13 (Proximity Label-MS), TTC13 (Proximity Label-MS), TTC13 (Proximity Label-MS), TTC13 (Proximity Label-MS), TTC13 (Affinity Capture-MS), TTC13 (Proximity Label-MS)

ESM2 similar proteins: A0JPE1, A4D0V7, D3Z2R5, O43916, P97259, Q08834, Q09328, Q1RLQ5, Q3TUA9, Q4V8A9, Q58CX7, Q5F349, Q5FVL3, Q5HZP7, Q5NDE4, Q5NDE5, Q5NDE7, Q5NDE8, Q5R634, Q5R9Q9, Q5RJQ0, Q5T7M9, Q5U3W1, Q5VUD6, Q640M6, Q68CR1, Q6DBY9, Q6DCL6, Q6Q2W4, Q80TS8, Q8C1F4, Q8C3I9, Q8N6G5, Q8NBP0, Q8NHY0, Q8R4G6, Q8R553, Q8WTR4, Q92179, Q95JJ0

Diamond homologs: A0A3L6DPG1, B0BN85, F8RP11, O13797, O59709, Q08446, Q0JL44, Q2KIK0, Q43468, Q55ED0, Q5WA76, Q7T3F7, Q8NBP0, Q9CX34, Q9SUR9, Q9SUT5, Q9Y2Z0, P38825, Q5R6Z8, Q5R8D8, Q99615, Q9QYI3, Q9STH1, O00592, Q04864, Q2U919, Q54IP0, Q5XEP2, Q6B4Z3, Q6UX73, Q8N769, Q9H2J1, Q9NV72

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 100 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
Antigen Presentation: Folding, assembly and peptide loading of class I MHC	5	31.8×	1e-04
Neutrophil degranulation	12	4.5×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	8	16.9×	1e-05
immune response	9	4.9×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	91
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3901 predictions. Top by Δscore:

Variant	Effect	Δscore
1:230907020:C:CC	acceptor_gain	1.0000
1:230907848:A:AC	donor_gain	1.0000
1:230907849:C:CC	donor_gain	1.0000
1:230908707:GTTAC:G	donor_loss	1.0000
1:230908708:TTA:T	donor_loss	1.0000
1:230908709:TA:T	donor_loss	1.0000
1:230908710:ACCT:A	donor_loss	1.0000
1:230908788:CTAA:C	acceptor_gain	1.0000
1:230908789:TAA:T	acceptor_gain	1.0000
1:230908790:AA:A	acceptor_gain	1.0000
1:230908792:C:CC	acceptor_gain	1.0000
1:230908937:CATA:C	donor_loss	1.0000
1:230908938:ATACC:A	donor_loss	1.0000
1:230908939:TACC:T	donor_loss	1.0000
1:230908940:A:T	donor_loss	1.0000
1:230908945:C:A	donor_gain	1.0000
1:230909016:TTACA:T	acceptor_gain	1.0000
1:230909017:TACA:T	acceptor_gain	1.0000
1:230909019:CA:C	acceptor_gain	1.0000
1:230909021:C:CC	acceptor_gain	1.0000
1:230911466:TTA:T	donor_loss	1.0000
1:230911467:TACC:T	donor_loss	1.0000
1:230911469:C:CA	donor_loss	1.0000
1:230911547:CTC:C	acceptor_gain	1.0000
1:230911550:CT:C	acceptor_loss	1.0000
1:230911551:T:C	acceptor_loss	1.0000
1:230912618:CCTA:C	donor_loss	1.0000
1:230912619:CTACC:C	donor_loss	1.0000
1:230912621:A:AC	donor_gain	1.0000
1:230912621:A:AT	donor_loss	1.0000

AlphaMissense

5621 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:230920526:A:G	L656P	1.000
1:230924848:A:G	W572R	1.000
1:230924848:A:T	W572R	1.000
1:230931388:C:A	G404W	1.000
1:230931388:C:G	G404R	1.000
1:230931388:C:T	G404R	1.000
1:230931424:C:A	G392W	1.000
1:230931424:C:G	G392R	1.000
1:230931424:C:T	G392R	1.000
1:230931437:G:C	C387W	1.000
1:230931438:C:T	C387Y	1.000
1:230931439:A:G	C387R	1.000
1:230931469:A:G	C377R	1.000
1:230933791:C:T	G324E	1.000
1:230933792:C:A	G324W	1.000
1:230933792:C:G	G324R	1.000
1:230933792:C:T	G324R	1.000
1:230933794:A:G	L323P	1.000
1:230933858:C:G	A302P	1.000
1:230939417:C:T	G290D	1.000
1:230939418:C:G	G290R	1.000
1:230939483:G:T	A268D	1.000
1:230940462:C:T	G256E	1.000
1:230940463:C:G	G256R	1.000
1:230940463:C:T	G256R	1.000
1:230940465:C:G	R255P	1.000
1:230940513:A:G	L239P	1.000
1:230940526:C:G	A235P	1.000
1:230943811:C:G	A223P	1.000
1:230943813:C:G	R222P	1.000

dbSNP variants (sampled 300 via entrez): RS1000019673 (1:230921926 C>T), RS1000023806 (1:230969247 G>A), RS1000033650 (1:230969479 C>T), RS1000060217 (1:230928066 G>A), RS1000077339 (1:230965781 G>A,C), RS1000161031 (1:230944048 T>G), RS1000322151 (1:230925539 C>A), RS1000375569 (1:230936951 T>C,G), RS1000409392 (1:230933096 C>A), RS1000434888 (1:230912110 T>C), RS1000446981 (1:230944346 T>C), RS1000482619 (1:230921498 C>T), RS1000483148 (1:230933299 T>C), RS1000528904 (1:230916785 C>G,T), RS1000589171 (1:230916507 C>T)

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

4 associations (top):

Study	Trait	p-value
GCST008154_79	Trunk fat mass	7.000000e-06
GCST90002383_152	Hematocrit	5.000000e-14
GCST90002384_31	Hemoglobin	1.000000e-10
GCST90002403_68	Red blood cell count	1.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004348	hematocrit
EFO:0004509	hemoglobin measurement
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	3
Valproic Acid	affects expression, decreases methylation, increases expression	3
Arsenic	increases expression, affects cotreatment, decreases expression, increases abundance	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
lead acetate	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
nickel sulfate	decreases expression	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
corosolic acid	increases expression	1
abrine	decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Disulfiram	affects binding, increases expression	1
Doxorubicin	decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Asbestos, Crocidolite	increases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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