TTC38

Summary

TTC38 (tetratricopeptide repeat domain 38, HGNC:26082) is a protein-coding gene on chromosome 22q13.31, encoding Tetratricopeptide repeat protein 38 (Q5R3I4).

Located in extracellular exosome.

Source: NCBI Gene 55020 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 99 total
• MANE Select transcript: NM_017931

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26082
Approved symbol	TTC38
Name	tetratricopeptide repeat domain 38
Location	22q13.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20699
Ensembl gene	ENSG00000075234
Ensembl biotype	protein_coding
Entrez	55020

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 14 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron

ENST00000381031, ENST00000417709, ENST00000421359, ENST00000422713, ENST00000451998, ENST00000475467, ENST00000629918, ENST00000857233, ENST00000857234, ENST00000857235, ENST00000857236, ENST00000857237, ENST00000857238, ENST00000857239, ENST00000857240, ENST00000857241, ENST00000857242, ENST00000960782

RefSeq mRNA: 1 — MANE Select: NM_017931 NM_017931

CCDS: CCDS43030

Canonical transcript exons

ENST00000381031 — 14 exons

Exon	Start	End
ENSE00000657281	46275248	46275421
ENSE00000657283	46278586	46278661
ENSE00000657284	46281599	46281718
ENSE00000657286	46285241	46285279
ENSE00000657287	46287073	46287154
ENSE00001250820	46268514	46268591
ENSE00001487274	46289826	46289899
ENSE00001487276	46289402	46289561
ENSE00001487282	46288423	46288588
ENSE00001934928	46292791	46294008
ENSE00003502346	46273898	46274069
ENSE00003512136	46283973	46284032
ENSE00003541086	46272335	46272416
ENSE00003686648	46268008	46268072

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 98.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0690 / max 312.4279, expressed in 1807 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
192799	18.1408	1804
192798	1.5905	1109
192802	0.2054	78
192804	0.0504	23
192803	0.0440	20
192797	0.0379	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	98.60	gold quality
mucosa of transverse colon	UBERON:0004991	97.46	gold quality
granulocyte	CL:0000094	97.15	gold quality
liver	UBERON:0002107	96.61	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.97	gold quality
transverse colon	UBERON:0001157	94.57	gold quality
nephron tubule	UBERON:0001231	94.24	gold quality
adult mammalian kidney	UBERON:0000082	94.21	gold quality
rectum	UBERON:0001052	94.01	gold quality
small intestine	UBERON:0002108	93.92	gold quality
jejunal mucosa	UBERON:0000399	93.67	gold quality
body of pancreas	UBERON:0001150	93.02	gold quality
body of stomach	UBERON:0001161	92.86	gold quality
duodenum	UBERON:0002114	92.80	gold quality
right ovary	UBERON:0002118	92.61	gold quality
kidney epithelium	UBERON:0004819	92.57	gold quality
intestine	UBERON:0000160	92.13	gold quality
left ovary	UBERON:0002119	92.12	gold quality
metanephros cortex	UBERON:0010533	91.97	gold quality
kidney	UBERON:0002113	91.94	gold quality
colon	UBERON:0001155	91.69	gold quality
cortex of kidney	UBERON:0001225	91.65	gold quality
large intestine	UBERON:0000059	91.63	gold quality
colonic mucosa	UBERON:0000317	90.89	gold quality
right adrenal gland cortex	UBERON:0035827	90.80	gold quality
left adrenal gland cortex	UBERON:0035825	90.76	gold quality
renal glomerulus	UBERON:0000074	90.65	gold quality
right adrenal gland	UBERON:0001233	90.57	gold quality
apex of heart	UBERON:0002098	90.55	gold quality
metanephric glomerulus	UBERON:0004736	90.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-122	yes	48.25
E-MTAB-6678	yes	10.09
E-ANND-3	yes	8.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting TTC38, 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-3064-3P	100.00	70.09	1254
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-661	99.09	65.94	2062

Literature-anchored findings (GeneRIF, showing 1)

• we proposed that four newly identified peripheral blood mononuclear cells-derived genes( DHRS3, TTC38, SAP30BP and LPIN2 )could be integrated with previously reported rheumatoid arthritis (RA)-associated genes to monitor and/or diagnose RA. (PMID:28371410)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ttc38	ENSDARG00000042188
mus_musculus	Ttc38	ENSMUSG00000035944
rattus_norvegicus	Ttc38	ENSRNOG00000015916
caenorhabditis_elegans		WBGENE00013215
caenorhabditis_elegans		WBGENE00013216

Protein

Protein identifiers

Tetratricopeptide repeat protein 38 — Q5R3I4 (reviewed: Q5R3I4)

All UniProt accessions (5): Q5R3I4, A9UJP8, F8WBU8, H7C089, H7C2L7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the TTC38 family.

RefSeq proteins (1): NP_060401* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR033891	TTC38	Family

UniProt features (8 total): repeat 3, modified residue 2, initiator methionine 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5R3I4-F1	96.54	0.95

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): 2, 5

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GNF2_IL2RB, CHANG_IMMORTALIZED_BY_HPV31_UP, PARENT_MTOR_SIGNALING_UP, GNF2_PTPN4, chr22q13, NUYTTEN_NIPP1_TARGETS_DN, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, WHITFIELD_CELL_CYCLE_G2, RATTENBACHER_BOUND_BY_CELF1, ZWANG_DOWN_BY_2ND_EGF_PULSE, ALK_DN.V1_DN

GO Biological Process (0):

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

GO Cellular Component (1): extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
extracellular vesicle	1

Protein interactions and networks

STRING

514 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC38	MANSC4	A6NHS7	590
TTC38	LRIT2	A6NDA9	557
TTC38	KIAA1958	Q8N8K9	547
TTC38	LRIT1	Q9P2V4	525
TTC38	SIRAL2	Q9NWS6	519
TTC38	ZCCHC17	Q9NP64	484
TTC38	ABHD14B	Q96IU4	479
TTC38	HDHD2	Q9H0R4	443
TTC38	TRMU	O75648	442
TTC38	DDX28	Q9NUL7	436
TTC38	CLIP3	Q96DZ5	432
TTC38	DHRS1	Q96LJ7	430
TTC38	TTC36	A6NLP5	416
TTC38	ENOSF1	Q7L5Y1	387
TTC38	GTSE1	Q9NYZ3	375

IntAct

18 interactions, top by confidence:

A	B	Type	Score
FBXO7	SKP1	psi-mi:“MI:0914”(association)	0.900
SEMA3C	TTC38	psi-mi:“MI:0915”(physical association)	0.500
PFDN1	TTC38	psi-mi:“MI:0915”(physical association)	0.370
TTC38	TK1	psi-mi:“MI:0915”(physical association)	0.370
	VWA8	psi-mi:“MI:0914”(association)	0.350
PB2	SEC15L3	psi-mi:“MI:0914”(association)	0.350
IQCN	TARSL2	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
IQCN	TARS3	psi-mi:“MI:0914”(association)	0.350
P2RY10	POTEF	psi-mi:“MI:0914”(association)	0.350
SNAPC4	PIK3C2A	psi-mi:“MI:0914”(association)	0.350
SEMA3C	ZZEF1	psi-mi:“MI:0914”(association)	0.350
FBXO7	SKAP2	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
SLC22A11	CNOT1	psi-mi:“MI:0914”(association)	0.350
SLC27A6	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (29): PFAS (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Co-fractionation), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS), TTC38 (Affinity Capture-MS)

ESM2 similar proteins: A1A5Y5, A2ACP1, A2VD82, A3KMP2, A3KPN8, B3MCZ5, B3NRC6, B4G9X6, B4GDM5, B4HR14, B4JVG7, B4JW83, B4KT65, B4LJT9, B4LNQ8, B4P6M6, B4QFD2, D3ZC96, I1R9A9, O22585, O64407, O65015, P10538, Q09266, Q13564, Q1LXE6, Q24902, Q28D40, Q28DB0, Q292F0, Q4R3L6, Q5R3I4, Q5RFF7, Q5SRH9, Q5U3P0, Q5XHH9, Q5ZIE6, Q6DIV2, Q6INC1, Q6NTW6

Diamond homologs: A2VD82, A3KMP2, A3KPN8, Q5R3I4, Q5RFF7, Q6DIV2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2538 predictions. Top by Δscore:

Variant	Effect	Δscore
22:46272333:A:AG	acceptor_gain	1.0000
22:46272334:G:GC	acceptor_gain	1.0000
22:46272334:GT:G	acceptor_gain	1.0000
22:46272334:GTAT:G	acceptor_gain	1.0000
22:46272412:CTTTG:C	donor_gain	1.0000
22:46272415:TGGT:T	donor_loss	1.0000
22:46272417:GTGA:G	donor_loss	1.0000
22:46272418:TGA:T	donor_loss	1.0000
22:46272419:GAG:G	donor_loss	1.0000
22:46273894:CCAGT:C	acceptor_loss	1.0000
22:46273896:A:AG	acceptor_gain	1.0000
22:46273897:G:GG	acceptor_gain	1.0000
22:46274049:A:AG	donor_gain	1.0000
22:46274050:G:GG	donor_gain	1.0000
22:46275242:TTCCA:T	acceptor_loss	1.0000
22:46275243:TCCA:T	acceptor_loss	1.0000
22:46275244:CCAG:C	acceptor_loss	1.0000
22:46275245:CAG:C	acceptor_loss	1.0000
22:46275246:A:AG	acceptor_gain	1.0000
22:46275246:A:T	acceptor_loss	1.0000
22:46275247:G:GG	acceptor_gain	1.0000
22:46275418:GCAG:G	donor_gain	1.0000
22:46275420:AGGT:A	donor_loss	1.0000
22:46275422:G:C	donor_loss	1.0000
22:46275423:T:A	donor_loss	1.0000
22:46278581:TTTA:T	acceptor_loss	1.0000
22:46278582:TTA:T	acceptor_loss	1.0000
22:46278583:TA:T	acceptor_loss	1.0000
22:46278584:A:AG	acceptor_gain	1.0000
22:46278584:AGCT:A	acceptor_loss	1.0000

AlphaMissense

3082 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:46278608:T:C	F188L	0.996
22:46278610:T:A	F188L	0.996
22:46278610:T:G	F188L	0.996
22:46289550:A:C	S411R	0.996
22:46289552:C:A	S411R	0.996
22:46289552:C:G	S411R	0.996
22:46289561:G:C	Q414H	0.996
22:46289561:G:T	Q414H	0.996
22:46283994:C:G	H253D	0.994
22:46281635:C:G	H218D	0.993
22:46278612:G:A	G189D	0.992
22:46281626:T:A	W215R	0.992
22:46281626:T:C	W215R	0.992
22:46289551:G:T	S411I	0.992
22:46292808:G:C	R445P	0.992
22:46275273:T:A	W131R	0.991
22:46275273:T:C	W131R	0.991
22:46278596:G:C	G184R	0.991
22:46281647:C:G	H222D	0.991
22:46284006:C:G	H257D	0.991
22:46275303:G:C	D141H	0.990
22:46281645:C:A	A221D	0.989
22:46284003:T:A	W256R	0.989
22:46284003:T:C	W256R	0.989
22:46287139:C:A	R301S	0.989
22:46281648:A:C	H222P	0.988
22:46281649:C:A	H222Q	0.988
22:46281649:C:G	H222Q	0.988
22:46281713:T:A	W244R	0.988
22:46281713:T:C	W244R	0.988

dbSNP variants (sampled 300 via entrez): RS1000008768 (22:46272963 T>C), RS1000078050 (22:46279491 G>A), RS1000140505 (22:46292487 A>G), RS1000271083 (22:46278626 A>G), RS1000299299 (22:46267584 G>A), RS1000337691 (22:46283714 T>G), RS1000433996 (22:46284091 A>T), RS1000499817 (22:46277330 C>T), RS1000885530 (22:46279646 T>C), RS1000951022 (22:46268822 C>G,T), RS1000955250 (22:46288678 C>T), RS1001108184 (22:46268993 A>G), RS1001131009 (22:46267625 C>G), RS1001175263 (22:46292562 C>G), RS1001205811 (22:46293894 G>A)

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

1 associations (top):

Study	Trait	p-value
GCST009733_210	Urinary metabolite levels in chronic kidney disease	6.000000e-46

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement

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
bisphenol A	decreases methylation, increases expression	2
Acetaminophen	decreases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
Smoke	decreases expression, increases expression	2
Valproic Acid	affects expression, decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
TAK-243	increases sumoylation	1
2,4,6-tribromophenol	increases expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	increases expression	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	increases expression	1
(+)-JQ1 compound	decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Methapyrilene	increases methylation	1
Rotenone	decreases expression	1
Cyclosporine	decreases expression	1
Sodium Selenite	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TV06	HAP1 TTC38 (-) 1	Cancer cell line	Male
CVCL_XU80	HAP1 TTC38 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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