TTC9B

Summary

TTC9B (tetratricopeptide repeat domain 9B, HGNC:26395) is a protein-coding gene on chromosome 19q13.2, encoding Tetratricopeptide repeat protein 9B (Q8N6N2).

At a glance

• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_152479

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26395
Approved symbol	TTC9B
Name	tetratricopeptide repeat domain 9B
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30373
Ensembl gene	ENSG00000174521
Ensembl biotype	protein_coding
Entrez	148014

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000311308, ENST00000593586, ENST00000854610, ENST00000959521

RefSeq mRNA: 1 — MANE Select: NM_152479 NM_152479

CCDS: CCDS12550

Canonical transcript exons

ENST00000311308 — 3 exons

Exon	Start	End
ENSE00001197731	40217955	40218384
ENSE00001405467	40217187	40217369
ENSE00001408009	40216058	40216272

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 97.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.2685 / max 216.3833, expressed in 167 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180947	2.2685	167

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	97.84	gold quality
cerebellar hemisphere	UBERON:0002245	97.50	gold quality
cerebellar cortex	UBERON:0002129	97.49	gold quality
cortical plate	UBERON:0005343	97.46	gold quality
amygdala	UBERON:0001876	97.19	gold quality
right frontal lobe	UBERON:0002810	96.79	gold quality
cerebellum	UBERON:0002037	96.70	gold quality
anterior cingulate cortex	UBERON:0009835	96.65	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.38	gold quality
cerebellar vermis	UBERON:0004720	94.31	gold quality
temporal lobe	UBERON:0001871	93.40	gold quality
neocortex	UBERON:0001950	93.32	gold quality
frontal cortex	UBERON:0001870	92.99	gold quality
cerebral cortex	UBERON:0000956	92.79	gold quality
hypothalamus	UBERON:0001898	92.54	gold quality
prefrontal cortex	UBERON:0000451	92.25	gold quality
tendon of biceps brachii	UBERON:0008188	91.13	silver quality
nucleus accumbens	UBERON:0001882	90.69	gold quality
Ammon’s horn	UBERON:0001954	90.43	gold quality
primary visual cortex	UBERON:0002436	90.23	gold quality
endothelial cell	CL:0000115	89.43	silver quality
occipital lobe	UBERON:0002021	89.24	gold quality
brain	UBERON:0000955	89.22	gold quality
putamen	UBERON:0001874	88.78	gold quality
forebrain	UBERON:0001890	88.53	gold quality
superior frontal gyrus	UBERON:0002661	88.41	gold quality
entorhinal cortex	UBERON:0002728	87.86	gold quality
ganglionic eminence	UBERON:0004023	87.61	gold quality
pons	UBERON:0000988	87.15	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-11121	yes	526.86
E-MTAB-9435	yes	442.78
E-HCAD-5	yes	52.11
E-ANND-3	no	0.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting TTC9B, 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-6758-5P	100.00	66.21	1470
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-5190	99.15	67.76	1234
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-4710	98.61	65.96	1048
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-1226-3P	97.51	66.32	1063

Literature-anchored findings (GeneRIF, showing 2)

• found two biomarker loci at HP1BP3 and TTC9B, which predicted postpartum depression (PMID:24317310)
• DNA methylation at early antenatal time points associated with changes in estradiol and allopregnanolone and postpartum depression (PMID:26503311)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ttc9b	ENSDARG00000068421
mus_musculus	Ttc9b	ENSMUSG00000007944
rattus_norvegicus	Ttc9b	ENSRNOG00000018850
caenorhabditis_elegans		WBGENE00001429
caenorhabditis_elegans	fkb-5	WBGENE00001430

Paralogs (18): FKBP4 (ENSG00000004478), FKBP6 (ENSG00000077800), FKBP7 (ENSG00000079150), FKBP1A (ENSG00000088832), FKBP5 (ENSG00000096060), FKBP3 (ENSG00000100442), FKBP8 (ENSG00000105701), FKBP14 (ENSG00000106080), FKBP15 (ENSG00000119321), FKBP1B (ENSG00000119782), FKBP9 (ENSG00000122642), TTC9 (ENSG00000133985), FKBP11 (ENSG00000134285), FKBP10 (ENSG00000141756), TTC9C (ENSG00000162222), FKBP2 (ENSG00000173486), FKBP1C (ENSG00000198225), FKBPL (ENSG00000204315)

Protein

Protein identifiers

Tetratricopeptide repeat protein 9B — Q8N6N2 (reviewed: Q8N6N2)

All UniProt accessions (1): Q8N6N2

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. May be due to an intron retention.

Similarity. Belongs to the TTC9 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N6N2-1	1	yes
Q8N6N2-2	2

RefSeq proteins (1): NP_689692* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR013105	TPR_2	Repeat
IPR019734	TPR_rpt	Repeat
IPR039663	AIP/AIPL1/TTC9	Family

Pfam: PF07719

UniProt features (11 total): repeat 2, region of interest 2, compositionally biased region 2, modified residue 2, chain 1, sequence variant 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6N2-F1	77.35	0.51

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 (2): 7, 27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): GGGTGGRR_PAX4_03, GATA1_01, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, MEISSNER_NPC_HCP_WITH_H3K4ME2, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, PEDRIOLI_MIR31_TARGETS_UP, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_12H_UP, E2F5_TARGET_GENES, MIER1_TARGET_GENES, PTPRA_TARGET_GENES, RYBP_TARGET_GENES, ZNF322_TARGET_GENES, MIR1226_3P

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

GO Molecular Function (2): molecular_function (GO:0003674), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

2304 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC9B	HP1BP3	Q5SSJ5	799
TTC9B	DMAC2	Q9NW81	611
TTC9B	IRGQ	Q8WZA9	558
TTC9B	ABRACL	Q9P1F3	504
TTC9B	LRFN3	Q9BTN0	500
TTC9B	TULP2	O00295	498
TTC9B	ERICH1	Q86X53	464
TTC9B	SBK1	Q52WX2	451
TTC9B	C19orf47	Q8N9M1	431
TTC9B	HIPK4	Q8NE63	428
TTC9B	ACTMAP	Q5BKX5	418
TTC9B	ZNF668	Q96K58	407
TTC9B	MEX3B	Q6ZN04	404
TTC9B	RTBDN	Q9BSG5	401
TTC9B	ZNF780A	O75290	371

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TTC9B	LTB4R2	psi-mi:“MI:0915”(physical association)	0.370
ERBB2	TTC9B	psi-mi:“MI:0915”(physical association)	0.370
TTC9B	PLCG1	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): TTC9B (Two-hybrid), PLCG1 (Affinity Capture-MS), CLTCL1 (Affinity Capture-MS), PPFIA1 (Affinity Capture-MS), HSPA4 (Affinity Capture-MS), TTC9B (Two-hybrid), PLCG1 (Affinity Capture-MS), PPFIA1 (Affinity Capture-MS), CLTCL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: A4IFF3, A4IHU6, O35450, O35465, P26882, P53691, Q08752, Q14318, Q3B7U9, Q3V038, Q5RAP0, Q6DGG0, Q6MG81, Q6P5P3, Q7DMA9, Q810A3, Q8N5M4, Q8N6N2, Q92623, Q9BGT1, Q9CR16, Q9D6E4, Q9H3U1, Q38931, Q43207, Q9LDC0, Q9VDE4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

812 predictions. Top by Δscore:

Variant	Effect	Δscore
19:40217185:A:AC	donor_gain	1.0000
19:40217185:AC:A	donor_gain	1.0000
19:40217186:C:CC	donor_gain	1.0000
19:40217186:CC:C	donor_gain	1.0000
19:40217186:CCT:C	donor_gain	1.0000
19:40217186:CCTG:C	donor_gain	1.0000
19:40217981:T:TA	donor_gain	1.0000
19:40216273:C:CC	acceptor_gain	0.9900
19:40217183:TCA:T	donor_gain	0.9900
19:40217184:CACC:C	donor_gain	0.9900
19:40217185:ACCT:A	donor_gain	0.9900
19:40217186:CCTGT:C	donor_gain	0.9900
19:40217692:C:CT	acceptor_gain	0.9900
19:40217951:GTA:G	donor_loss	0.9900
19:40217952:TA:T	donor_loss	0.9900
19:40217953:A:AC	donor_gain	0.9900
19:40217953:AC:A	donor_gain	0.9900
19:40217954:C:CC	donor_gain	0.9900
19:40217954:C:CT	donor_loss	0.9900
19:40217954:CC:C	donor_gain	0.9900
19:40216270:TGT:T	acceptor_gain	0.9800
19:40217370:C:CC	acceptor_gain	0.9800
19:40217693:A:T	acceptor_gain	0.9800
19:40216270:TGTCT:T	acceptor_loss	0.9700
19:40216272:TCTGC:T	acceptor_loss	0.9700
19:40216273:C:CG	acceptor_loss	0.9700
19:40216271:GT:G	acceptor_gain	0.9600
19:40217366:CAAG:C	acceptor_gain	0.9600
19:40217953:ACC:A	donor_gain	0.9600
19:40217954:CCC:C	donor_gain	0.9600

AlphaMissense

1508 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:40216245:A:G	L213P	1.000
19:40217216:A:G	L194P	1.000
19:40217250:G:C	H183D	1.000
19:40217253:A:C	Y182D	1.000
19:40217258:G:T	A180D	1.000
19:40217264:C:T	G178D	1.000
19:40217265:C:G	G178R	1.000
19:40217270:C:G	R176P	1.000
19:40217271:G:T	R176S	1.000
19:40217274:A:C	Y175D	1.000
19:40217281:C:A	K172N	1.000
19:40217281:C:G	K172N	1.000
19:40217317:A:C	C160W	1.000
19:40217318:C:T	C160Y	1.000
19:40217360:A:G	L146P	1.000
19:40217363:A:G	L145P	1.000
19:40217365:G:C	C144W	1.000
19:40217366:C:T	C144Y	1.000
19:40217367:A:G	C144R	1.000
19:40217960:A:G	L141P	1.000
19:40217960:A:T	L141H	1.000
19:40218104:A:G	L93P	1.000
19:40218115:G:C	H89Q	1.000
19:40218115:G:T	H89Q	1.000
19:40218117:G:C	H89D	1.000
19:40218117:G:T	H89N	1.000
19:40218120:A:C	Y88D	1.000
19:40218120:A:G	Y88H	1.000
19:40218125:C:T	G86D	1.000
19:40216255:A:C	Y210D	0.999

dbSNP variants (sampled 300 via entrez): RS1000490061 (19:40217548 C>A,T), RS1000752459 (19:40218558 C>G), RS1000819645 (19:40217357 T>C), RS1000995801 (19:40220234 G>A), RS1001225345 (19:40218805 A>G), RS1001360519 (19:40219815 C>T), RS1002828029 (19:40219998 A>C,G), RS1003000125 (19:40215563 C>A), RS1003260347 (19:40216843 G>A,C), RS1004498927 (19:40219709 C>A,G), RS1004590769 (19:40219226 G>A,T), RS1005209347 (19:40216633 C>T), RS1005368690 (19:40216813 G>T), RS1006832232 (19:40218642 C>T), RS1007009369 (19:40217833 G>A,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Vorinostat	decreases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	increases methylation	1
Lead	affects expression	1
Niclosamide	increases expression	1
Valproic Acid	increases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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