TTC39A

Summary

TTC39A (tetratricopeptide repeat domain 39A, HGNC:18657) is a protein-coding gene on chromosome 1p32.3, encoding Tetratricopeptide repeat protein 39A (Q5SRH9).

Located in centrosome.

Source: NCBI Gene 22996 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 81 total
• Phenotypes (HPO): 1
• MANE Select transcript: NM_001297663

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18657
Approved symbol	TTC39A
Name	tetratricopeptide repeat domain 39A
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0452, DEME-6
Ensembl gene	ENSG00000085831
Ensembl biotype	protein_coding
OMIM	619885
Entrez	22996

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 18 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000262675, ENST00000262676, ENST00000371747, ENST00000371750, ENST00000380849, ENST00000401051, ENST00000411642, ENST00000413473, ENST00000422925, ENST00000431927, ENST00000439482, ENST00000447632, ENST00000524442, ENST00000525906, ENST00000527205, ENST00000530004, ENST00000532836, ENST00000534098, ENST00000680290, ENST00000680460, ENST00000680483, ENST00000897167

RefSeq mRNA: 9 — MANE Select: NM_001297663 NM_001080494, NM_001144832, NM_001297662, NM_001297663, NM_001297664, NM_001297665, NM_001297666, NM_001297667, NM_001410793

CCDS: CCDS44143, CCDS44144, CCDS72789, CCDS72790, CCDS76162, CCDS76163, CCDS90953, CCDS90954

Canonical transcript exons

ENST00000680483 — 18 exons

Exon	Start	End
ENSE00000835623	51287258	51288280
ENSE00001130498	51305977	51306076
ENSE00001237505	51311254	51311321
ENSE00001237520	51312812	51312943
ENSE00001237539	51312119	51312195
ENSE00001456008	51330437	51330562
ENSE00001650121	51309261	51309325
ENSE00003479125	51301572	51301733
ENSE00003479532	51294391	51294511
ENSE00003479848	51290514	51290625
ENSE00003508941	51290005	51290119
ENSE00003616353	51305081	51305146
ENSE00003633626	51288839	51288955
ENSE00003670351	51302506	51302573
ENSE00003678430	51296079	51296170
ENSE00003694089	51321721	51321825
ENSE00003784284	51302357	51302416
ENSE00003791264	51303084	51303192

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 94.89.

FANTOM5 (CAGE): breadth broad, TPM avg 3.6440 / max 168.3860, expressed in 638 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12297	1.3983	476
12296	0.5519	253
12301	0.4239	130
12295	0.4114	109
12289	0.3595	123
12292	0.1727	35
12293	0.0946	34
12299	0.0678	34
12290	0.0472	16
12300	0.0387	26

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	94.89	gold quality
right testis	UBERON:0004534	94.64	gold quality
sperm	CL:0000019	94.45	gold quality
left testis	UBERON:0004533	94.40	gold quality
rectum	UBERON:0001052	92.40	gold quality
male germ cell	CL:0000015	91.99	gold quality
testis	UBERON:0000473	91.65	gold quality
mucosa of sigmoid colon	UBERON:0004993	91.46	gold quality
colonic mucosa	UBERON:0000317	90.73	gold quality
mucosa of transverse colon	UBERON:0004991	89.81	gold quality
bronchial epithelial cell	CL:0002328	87.98	gold quality
lower esophagus mucosa	UBERON:0035834	87.42	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.61	gold quality
epithelium of bronchus	UBERON:0002031	85.98	gold quality
gall bladder	UBERON:0002110	85.75	gold quality
pancreas	UBERON:0001264	85.74	gold quality
bronchus	UBERON:0002185	85.17	gold quality
esophagus mucosa	UBERON:0002469	85.13	gold quality
metanephros cortex	UBERON:0010533	85.09	gold quality
pancreatic ductal cell	CL:0002079	84.54	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.16	gold quality
cervix squamous epithelium	UBERON:0006922	84.11	silver quality
apex of heart	UBERON:0002098	84.02	gold quality
nasal cavity epithelium	UBERON:0005384	83.46	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.84	gold quality
heart left ventricle	UBERON:0002084	82.53	gold quality
right uterine tube	UBERON:0001302	82.52	gold quality
prostate gland	UBERON:0002367	82.42	gold quality
transverse colon	UBERON:0001157	82.32	gold quality
body of pancreas	UBERON:0001150	82.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	16.24

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP63

miRNA regulators (miRDB)

59 targeting TTC39A, 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-4262	100.00	73.26	3931
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-1207-5P	99.49	69.11	2983

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ttc39a	ENSDARG00000074126
mus_musculus	Ttc39a	ENSMUSG00000028555
rattus_norvegicus	Ttc39a	ENSRNOG00000047573
caenorhabditis_elegans		WBGENE00016314

Paralogs (2): TTC39B (ENSG00000155158), TTC39C (ENSG00000168234)

Protein

Protein identifiers

Tetratricopeptide repeat protein 39A — Q5SRH9 (reviewed: Q5SRH9)

Alternative names: Differentially expressed in MCF-7 with estradiol protein 6

All UniProt accessions (13): Q5SRH9, A0A0A0MRQ0, A0A0A0MSW9, A0A140VJY6, A0A7P0T922, A0A7P0T9F5, E9PAZ4, E9PHX9, E9PQ33, E9PQX3, F6WE04, F8W961, U5GXS1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the TTC39 family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q5SRH9-1	1	yes
Q5SRH9-2	2
Q5SRH9-3	3
Q5SRH9-4	4
Q5SRH9-5	5
Q5SRH9-6	6

RefSeq proteins (9): NP_001073963, NP_001138304, NP_001284591, NP_001284592, NP_001284593, NP_001284594, NP_001284595, NP_001284596, NP_001397722 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019412	IML2/TPR_39	Family
IPR019734	TPR_rpt	Repeat

Pfam: PF10300

UniProt features (13 total): splice variant 7, repeat 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SRH9-F1	87.50	0.72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 125 (showing top): GOZGIT_ESR1_TARGETS_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, PUJANA_CHEK2_PCC_NETWORK, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, GOCC_CENTROSOME, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, LEIN_MIDBRAIN_MARKERS, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, LINDGREN_BLADDER_CANCER_CLUSTER_1_DN, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP, DOANE_BREAST_CANCER_ESR1_UP, MEISSNER_NPC_HCP_WITH_H3K4ME2, FARMER_BREAST_CANCER_CLUSTER_6, PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP, CHYLA_CBFA2T3_TARGETS_DN

GO Biological Process (0):

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

GO Cellular Component (1): centrosome (GO:0005813)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
centriole	1
microtubule organizing center	1

Protein interactions and networks

STRING

353 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC39A	ZNF19	P17023	543
TTC39A	CCDC92	Q53HC0	499
TTC39A	CMTR1	Q8N1G2	478
TTC39A	NIPAL2	Q9H841	445
TTC39A	OSBPL9	Q96SU4	423
TTC39A	H0YL09	H0YL09	419
TTC39A	NXN	Q6DKJ4	414
TTC39A	ZDHHC23	Q8IYP9	400
TTC39A	SART3	Q15020	398
TTC39A	DCAF5	Q96JK2	390
TTC39A	UPK3BL1	B0FP48	384
TTC39A	KTI12	Q96EK9	377
TTC39A	PPM1H	Q9ULR3	353
TTC39A	CDKN2C	P42773	350
TTC39A	SLC37A1	P57057	343

IntAct

9 interactions, top by confidence:

A	B	Type	Score
M		psi-mi:“MI:0914”(association)	0.350
GYPA	HYKK	psi-mi:“MI:0914”(association)	0.350
C5AR1	TCAF2	psi-mi:“MI:0914”(association)	0.350
P2RY12	GPR89A	psi-mi:“MI:0914”(association)	0.350
S100A9	GNPAT	psi-mi:“MI:0914”(association)	0.350
TTC39A	METTL18	psi-mi:“MI:0914”(association)	0.350
ACKR2	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC4A5	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): TTC39A (Affinity Capture-MS), TTC39A (Affinity Capture-MS), TNIP1 (Two-hybrid), TTC39A (Affinity Capture-MS), TTC39A (Affinity Capture-MS), TTC39A (Affinity Capture-MS), TTC39A (Affinity Capture-MS), TTC39A (Affinity Capture-MS), LMNA (Affinity Capture-MS), TTC39A (Affinity Capture-MS), METTL18 (Affinity Capture-MS), TTC39A (Affinity Capture-MS), TTC39A (Co-fractionation), TTC39A (Co-fractionation), TTC39A (Affinity Capture-MS)

ESM2 similar proteins: A1A5Y5, A1Z6M6, A2ACP1, A7E727, A7SUU7, A8NY27, A8X419, D3ZC96, O13693, O42897, O61820, O94699, P34560, P40515, Q03560, Q09266, Q0VGK2, Q1LXE6, Q20255, Q28D40, Q28DB0, Q2TBN6, Q5AFF7, Q5FWP8, Q5JVF3, Q5SRH9, Q5U3P0, Q5VTQ0, Q5XHH9, Q60YJ7, Q61LA1, Q6BLG8, Q6CU37, Q6FIQ1, Q6INC1, Q7RXQ1, Q7SI58, Q8BFV2, Q8BYY4, Q8C0S4

Diamond homologs: A1A5Y5, A2ACP1, D3ZC96, Q09266, Q28D40, Q28DB0, Q5SRH9, Q5VTQ0, Q5XHH9, Q8BYY4, Q95LT8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2612 predictions. Top by Δscore:

Variant	Effect	Δscore
1:51288830:AAG:A	donor_gain	1.0000
1:51288832:GCCTT:G	donor_loss	1.0000
1:51288833:CCTTA:C	donor_loss	1.0000
1:51288834:CTTA:C	donor_loss	1.0000
1:51288836:TA:T	donor_loss	1.0000
1:51288837:A:AC	donor_gain	1.0000
1:51288838:C:CA	donor_gain	1.0000
1:51288838:CTTGG:C	donor_gain	1.0000
1:51288951:TTTCA:T	acceptor_gain	1.0000
1:51288952:TTCA:T	acceptor_gain	1.0000
1:51288953:TCA:T	acceptor_gain	1.0000
1:51288954:CA:C	acceptor_gain	1.0000
1:51288954:CAC:C	acceptor_gain	1.0000
1:51288956:C:CC	acceptor_gain	1.0000
1:51288956:C:CG	acceptor_loss	1.0000
1:51288957:T:A	acceptor_loss	1.0000
1:51288959:C:CT	acceptor_gain	1.0000
1:51290001:TTAC:T	donor_loss	1.0000
1:51290002:TACT:T	donor_loss	1.0000
1:51290003:A:AC	donor_gain	1.0000
1:51290003:ACTT:A	donor_loss	1.0000
1:51290004:C:CT	donor_gain	1.0000
1:51290004:CT:C	donor_gain	1.0000
1:51290004:CTT:C	donor_gain	1.0000
1:51290004:CTTG:C	donor_gain	1.0000
1:51290004:CTTGG:C	donor_gain	1.0000
1:51290115:GTTCT:G	acceptor_gain	1.0000
1:51290116:TTCT:T	acceptor_gain	1.0000
1:51290118:CT:C	acceptor_gain	1.0000
1:51290120:C:CC	acceptor_gain	1.0000

AlphaMissense

3805 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:51305094:A:G	F250S	1.000
1:51309303:A:T	I185N	1.000
1:51288236:C:G	R588P	0.999
1:51290610:A:G	W464R	0.999
1:51290610:A:T	W464R	0.999
1:51294442:C:A	K441N	0.999
1:51294442:C:G	K441N	0.999
1:51294446:C:G	R440P	0.999
1:51294452:G:T	A438D	0.999
1:51294479:C:T	G429E	0.999
1:51301652:A:G	W361R	0.999
1:51301652:A:T	W361R	0.999
1:51303173:A:G	L261P	0.999
1:51303186:C:A	G257W	0.999
1:51305093:A:C	F250L	0.999
1:51305093:A:T	F250L	0.999
1:51305095:A:G	F250L	0.999
1:51305097:C:T	G249E	0.999
1:51305130:G:A	P238L	0.999
1:51305130:G:C	P238R	0.999
1:51305978:A:G	L232P	0.999
1:51305983:G:C	F230L	0.999
1:51305983:G:T	F230L	0.999
1:51305985:A:G	F230L	0.999
1:51305990:C:T	G228E	0.999
1:51305991:C:A	G228W	0.999
1:51305996:C:T	G226D	0.999
1:51305997:C:G	G226R	0.999
1:51309265:A:C	Y198D	0.999
1:51309275:G:C	S194R	0.999

dbSNP variants (sampled 300 via entrez): RS1000121104 (1:51304705 C>A,G,T), RS1000135695 (1:51337455 C>T), RS1000142705 (1:51299194 G>C,T), RS1000271809 (1:51341214 C>T), RS1000335511 (1:51312679 C>A,G), RS1000373451 (1:51291202 T>G), RS1000403633 (1:51292826 A>T), RS1000441761 (1:51312275 G>C,T), RS1000452423 (1:51335099 G>A), RS1000494216 (1:51342097 C>T), RS1000554617 (1:51317070 T>C), RS1000587857 (1:51317595 A>G), RS1000658578 (1:51311025 G>A,C,T), RS1000746725 (1:51298468 A>G,T), RS1000895831 (1:51329900 C>A,T)

Disease associations

OMIM: gene MIM:619885 | disease phenotypes: MIM:194200

GenCC curated gene-disease

Mondo (1): Wolff-Parkinson-White syndrome (MONDO:0008685)

Orphanet (1): NON RARE IN EUROPE: Wolff-Parkinson-White syndrome (Orphanet:907)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0001716	Wolff-Parkinson-White syndrome

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004632_86	Lymphocyte percentage of white cells	6.000000e-09
GCST012227_1068	Hip circumference adjusted for BMI	3.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0008039	BMI-adjusted hip circumference

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D014927	Wolff-Parkinson-White Syndrome	C14.280.067.780.977; C14.280.123.750.977; C16.131.240.400.980

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
sodium arsenite	increases expression	2
entinostat	increases expression, affects cotreatment	2
(+)-JQ1 compound	decreases expression	2
Calcitriol	increases expression, affects cotreatment	2
Estradiol	increases expression, affects cotreatment, decreases expression, decreases reaction	2
Valproic Acid	increases methylation, affects expression, decreases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
Particulate Matter	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
sotorasib	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	decreases expression, increases activity, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	decreases expression	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Bortezomib	increases expression	1
Sunitinib	decreases expression	1
Doxorubicin	affects expression	1
Nickel	increases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	increases expression, affects cotreatment	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00251121	Not specified	COMPLETED	Routine Mini-invasive Electrophysiology Study for Patients Feeling Tachycardia, With a Negative Holter ECG
NCT00873470	Not specified	TERMINATED	Wolff-Parkinson-White Syndrome Anterograde Refractory Period of Accessory Duct
NCT03207373	Not specified	TERMINATED	Stress ECG Test for the Evaluation of the Risk of Sudden Cardiac Death in a Paediatric Cohort With WPW Pattern
NCT03301935	Not specified	COMPLETED	Risk Assessment in Patients With Symptomatic- and Asymptomatic Preexcitation
NCT03816033	Not specified	UNKNOWN	Cryotherapy Versus Radiofrequency Catheter Ablation Research Program
NCT04106622	Not specified	UNKNOWN	Accessory Pathway Antegrade Effective Refractory Period Among WPW Patients: the Risk in Relation to the Location
NCT06349109	Not specified	COMPLETED	Physical Activity in Children With Wolff-Parkinson-White Syndrome
NCT07435181	Not specified	NOT_YET_RECRUITING	Comparative Outcomes of Radiofrequency Ablation of Concealed and Manifest Accessory Pathways: a Single Center, Retrospective Observational Study