TTC31

Summary

TTC31 (tetratricopeptide repeat domain 31, HGNC:25759) is a protein-coding gene on chromosome 2p13.1, encoding Tetratricopeptide repeat protein 31 (Q49AM3).

At a glance

• Clinical variants (ClinVar): 96 total
• MANE Select transcript: NM_022492

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25759
Approved symbol	TTC31
Name	tetratricopeptide repeat domain 31
Location	2p13.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12788
Ensembl gene	ENSG00000115282
Ensembl biotype	protein_coding
Entrez	64427

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 17 protein_coding, 6 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000233623, ENST00000410003, ENST00000414247, ENST00000424122, ENST00000442235, ENST00000449459, ENST00000459957, ENST00000463189, ENST00000463704, ENST00000464241, ENST00000487623, ENST00000489152, ENST00000491252, ENST00000888463, ENST00000888464, ENST00000888465, ENST00000888466, ENST00000888467, ENST00000888468, ENST00000888469, ENST00000888470, ENST00000888471, ENST00000888472, ENST00000933488, ENST00000933489, ENST00000933490

RefSeq mRNA: 15 — MANE Select: NM_022492 NM_001376129, NM_001376130, NM_001376132, NM_001376133, NM_001376134, NM_001376135, NM_001376136, NM_001376137, NM_001376138, NM_001376139, NM_001376140, NM_001376141, NM_001376144, NM_001376145, NM_022492

CCDS: CCDS42701

Canonical transcript exons

ENST00000233623 — 13 exons

Exon	Start	End
ENSE00001888883	74492922	74494559
ENSE00003480464	74492304	74492445
ENSE00003505605	74492646	74492747
ENSE00003515930	74490656	74490739
ENSE00003533913	74491295	74491375
ENSE00003534934	74492004	74492055
ENSE00003563242	74491128	74491184
ENSE00003567329	74492139	74492229
ENSE00003598801	74491481	74491672
ENSE00003611742	74483081	74483135
ENSE00003636336	74490025	74490127
ENSE00003657628	74483322	74483410
ENSE00003729242	74490244	74490473

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 92.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1845 / max 165.9154, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
21030	15.1845	1803

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	92.61	gold quality
right lobe of liver	UBERON:0001114	92.25	gold quality
granulocyte	CL:0000094	91.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	88.82	gold quality
spleen	UBERON:0002106	88.00	gold quality
small intestine	UBERON:0002108	87.92	gold quality
jejunal mucosa	UBERON:0000399	87.36	gold quality
transverse colon	UBERON:0001157	87.30	gold quality
liver	UBERON:0002107	87.09	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.95	gold quality
body of stomach	UBERON:0001161	86.74	gold quality
apex of heart	UBERON:0002098	86.64	gold quality
metanephros cortex	UBERON:0010533	86.62	gold quality
right lobe of thyroid gland	UBERON:0001119	86.42	gold quality
body of uterus	UBERON:0009853	86.41	gold quality
body of pancreas	UBERON:0001150	86.39	gold quality
right ovary	UBERON:0002118	86.35	gold quality
left ovary	UBERON:0002119	86.34	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	86.14	gold quality
vermiform appendix	UBERON:0001154	86.11	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.00	gold quality
lower esophagus	UBERON:0013473	85.99	gold quality
left lobe of thyroid gland	UBERON:0001120	85.92	gold quality
leukocyte	CL:0000738	85.61	gold quality
monocyte	CL:0000576	85.58	gold quality
mononuclear cell	CL:0000842	85.56	gold quality
right adrenal gland cortex	UBERON:0035827	85.53	gold quality
endocervix	UBERON:0000458	85.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.51	gold quality
right adrenal gland	UBERON:0001233	85.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

82 targeting TTC31, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4731-5P	99.89	67.23	2537

Literature-anchored findings (GeneRIF, showing 1)

• A fragment of the CCDC142-TTC31 intergenic region was cloned; this fragment functions as bidirectional promoter. (PMID:21790010)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-33c12.4	ENSDARG00000057890
drosophila_melanogaster	unc-45	FBGN0288846
caenorhabditis_elegans		WBGENE00006781

Paralogs (18): RPAP3 (ENSG00000005175), TOMM34 (ENSG00000025772), ST13 (ENSG00000100380), STUB1 (ENSG00000103266), SPAG1 (ENSG00000104450), SGTA (ENSG00000104969), TTC1 (ENSG00000113312), UNC45A (ENSG00000140553), UNC45B (ENSG00000141161), SPATA16 (ENSG00000144962), TTC12 (ENSG00000149292), TOMM70 (ENSG00000154174), SUGT1 (ENSG00000165416), STIP1 (ENSG00000168439), TTC32 (ENSG00000183891), SGTB (ENSG00000197860), TTC4 (ENSG00000243725), DNAAF4 (ENSG00000256061)

Protein

Protein identifiers

Tetratricopeptide repeat protein 31 — Q49AM3 (reviewed: Q49AM3)

All UniProt accessions (4): Q49AM3, F8VVP0, G5E9H3, H7BZ54

Isoforms (2)

UniProt ID	Names	Canonical?
Q49AM3-1	1	yes
Q49AM3-2	2

RefSeq proteins (15): NP_001363058, NP_001363059, NP_001363061, NP_001363062, NP_001363063, NP_001363064, NP_001363065, NP_001363066, NP_001363067, NP_001363068, NP_001363069, NP_001363070, NP_001363073, NP_001363074, NP_071937* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat

Pfam: PF13432

UniProt features (18 total): repeat 3, sequence conflict 3, region of interest 3, splice variant 2, sequence variant 2, compositionally biased region 2, chain 1, modified residue 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q49AM3-F1	61.06	0.29

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 (1): 278

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, GNF2_DDX5, chr2p13, WHITFIELD_CELL_CYCLE_S, ARNT2_TARGET_GENES, CIITA_TARGET_GENES, DIDO1_TARGET_GENES, HOXB4_TARGET_GENES, LHX9_TARGET_GENES, ZNF407_TARGET_GENES, MIR153_5P, MIR6833_3P, MIR4768_5P, MIR3166, MIR1273H_3P

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

1614 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC31	CCDC142	Q17RM4	670
TTC31	DQX1	Q8TE96	608
TTC31	AUP1	Q9Y679	540
TTC31	C2orf81	A6NN90	476
TTC31	REXO5	Q96IC2	455
TTC31	PCGF1	Q9BSM1	449
TTC31	TTC32	Q5I0X7	400
TTC31	TTC14	Q96N46	400
TTC31	TTC13	Q8NBP0	399
TTC31	WDR54	Q9H977	397
TTC31	AMMECR1L	Q6DCA0	394
TTC31	SEMA4F	O95754	383
TTC31	WDR11	Q9BZH6	382
TTC31	Q8WV35	Q8WV35	375
TTC31	REP15	Q6BDI9	371

IntAct

12 interactions, top by confidence:

A	B	Type	Score
PHF19	EED	psi-mi:“MI:0914”(association)	0.730
IFI30	PRC1	psi-mi:“MI:0914”(association)	0.530
SLC31A1	C2orf72	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
NXF2B	MEIOC	psi-mi:“MI:0914”(association)	0.350
LZTS2	MYO9A	psi-mi:“MI:0914”(association)	0.350
ZNF460	ZNF320	psi-mi:“MI:0914”(association)	0.350
CPEB1	CNOT1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (32): TTC31 (Affinity Capture-MS), TTC31 (Synthetic Growth Defect), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Affinity Capture-MS), TTC31 (Proximity Label-MS)

ESM2 similar proteins: A1L443, A2IDD5, A4IFI1, A6NJZ7, A6NNL0, A6NNM3, A8MT33, B1AL46, D3Z5T1, O95153, Q2M3G4, Q2T9R2, Q3TVI4, Q3TYX8, Q49AM3, Q4KLY2, Q569K6, Q5JTD0, Q5JXC2, Q5SSQ6, Q5SW24, Q5VT03, Q5VZR2, Q6ZNE9, Q7TN08, Q7TNF8, Q7Z591, Q80VJ8, Q810H6, Q811T9, Q86SX3, Q8C963, Q8CB62, Q8CII8, Q8IVF1, Q8IXR5, Q8N0S2, Q8N137, Q8N205, Q8N6L0

Diamond homologs: A0A3L6DPG1, A4K2V0, A6HD62, A6ZRW3, D3ZSP7, D7REX8, F1RBN2, F4IRM4, F8RP11, O13754, O13797, O14085, O14217, O16259, O35814, O43049, O54981, O88196, O95801, P07213, P0CT30, P15705, P23231, P25407, P31948, P38825, P50503, P53041, P53042, P53804, Q12118, Q28IV3, Q2U919, Q32NU8, Q3KRD5, Q3ZBR5, Q3ZBZ8, Q43468, Q496Y0, Q49AM3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1589 predictions. Top by Δscore:

Variant	Effect	Δscore
2:74483320:A:AG	acceptor_gain	1.0000
2:74483321:G:GG	acceptor_gain	1.0000
2:74490095:G:GT	donor_gain	1.0000
2:74490132:G:T	donor_gain	1.0000
2:74490472:AGG:A	donor_loss	1.0000
2:74490473:GGTG:G	donor_loss	1.0000
2:74490474:GTGA:G	donor_loss	1.0000
2:74490475:T:G	donor_loss	1.0000
2:74490632:T:TA	acceptor_gain	1.0000
2:74490636:ACCT:A	acceptor_gain	1.0000
2:74490639:T:A	acceptor_gain	1.0000
2:74490646:C:CA	acceptor_gain	1.0000
2:74490653:CA:C	acceptor_loss	1.0000
2:74490654:A:AC	acceptor_loss	1.0000
2:74490654:A:AG	acceptor_gain	1.0000
2:74490654:AG:A	acceptor_gain	1.0000
2:74490655:G:GA	acceptor_gain	1.0000
2:74490655:GG:G	acceptor_gain	1.0000
2:74490733:G:GT	donor_gain	1.0000
2:74490736:G:GT	donor_gain	1.0000
2:74490737:A:T	donor_gain	1.0000
2:74490769:G:T	donor_gain	1.0000
2:74491126:A:AG	acceptor_gain	1.0000
2:74491127:G:GG	acceptor_gain	1.0000
2:74491127:GC:G	acceptor_gain	1.0000
2:74491185:G:GA	donor_loss	1.0000
2:74491283:T:G	acceptor_gain	1.0000
2:74491293:A:AG	acceptor_gain	1.0000
2:74491293:AG:A	acceptor_gain	1.0000
2:74491294:G:GG	acceptor_gain	1.0000

AlphaMissense

3322 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:74492317:C:A	R345S	0.989
2:74492423:G:A	G380D	0.986
2:74492671:T:C	F396S	0.986
2:74492413:T:C	F377L	0.985
2:74492415:C:A	F377L	0.985
2:74492415:C:G	F377L	0.985
2:74492398:T:A	W372R	0.984
2:74492398:T:C	W372R	0.984
2:74492326:T:C	C348R	0.983
2:74492327:G:A	C348Y	0.980
2:74492328:C:G	C348W	0.980
2:74492320:T:C	S346P	0.979
2:74492670:T:C	F396L	0.978
2:74492672:T:A	F396L	0.978
2:74492672:T:G	F396L	0.978
2:74492321:C:T	S346F	0.977
2:74492658:G:C	A392P	0.976
2:74492145:G:A	G312D	0.975
2:74492201:G:C	A331P	0.975
2:74492318:G:C	R345P	0.975
2:74492378:C:A	A365D	0.975
2:74492193:T:C	F328S	0.974
2:74492368:G:C	A362P	0.974
2:74492400:G:C	W372C	0.974
2:74492400:G:T	W372C	0.974
2:74492423:G:T	G380V	0.974
2:74491505:T:C	F237L	0.973
2:74491507:T:A	F237L	0.973
2:74491507:T:G	F237L	0.973
2:74492312:G:A	G343E	0.973

dbSNP variants (sampled 300 via entrez): RS1000074070 (2:74485979 C>T), RS1000914543 (2:74485835 C>T), RS1001077083 (2:74487599 G>A), RS1001245829 (2:74494562 G>A), RS1001365143 (2:74481282 G>A), RS1001677482 (2:74494251 A>G), RS1002335268 (2:74482980 T>C), RS1002936676 (2:74484341 G>A,T), RS1003067558 (2:74490937 C>G), RS1003441650 (2:74494840 T>G), RS1003532816 (2:74481510 C>G), RS1003590800 (2:74494488 G>A), RS1004082204 (2:74488939 C>T), RS1004205740 (2:74481731 C>A,G), RS1004405969 (2:74487719 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	3
Acetaminophen	decreases expression, increases expression	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
Leflunomide	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	increases abundance, affects cotreatment, decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Selenium	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Vitamin E	decreases expression, affects cotreatment	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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