TTC23L

Summary

TTC23L (tetratricopeptide repeat domain 23 like, HGNC:26355) is a protein-coding gene on chromosome 5p13.2, encoding Tetratricopeptide repeat protein 23-like (Q6PF05).

Predicted to be involved in response to endoplasmic reticulum stress. Predicted to be located in cytoplasm; microtubule cytoskeleton; and midbody.

Source: NCBI Gene 153657 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_144725

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26355
Approved symbol	TTC23L
Name	tetratricopeptide repeat domain 23 like
Location	5p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25439
Ensembl gene	ENSG00000205838
Ensembl biotype	protein_coding
OMIM	616344
Entrez	153657

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000502674, ENST00000502782, ENST00000505624, ENST00000506758, ENST00000508377, ENST00000508722, ENST00000514080, ENST00000610313, ENST00000638320, ENST00000698543

RefSeq mRNA: 6 — MANE Select: NM_144725 NM_001317949, NM_001386169, NM_001386170, NM_001386171, NM_001386172, NM_144725

CCDS: CCDS54840

Canonical transcript exons

ENST00000505624 — 11 exons

Exon	Start	End
ENSE00001691591	34896770	34896875
ENSE00002090431	34839164	34839259
ENSE00003539509	34862898	34863054
ENSE00003542179	34850185	34850308
ENSE00003546476	34840665	34840739
ENSE00003587759	34868905	34869013
ENSE00003591184	34864437	34864562
ENSE00003616084	34845487	34845673
ENSE00003630883	34866892	34867069
ENSE00003691183	34880181	34880308
ENSE00003978140	34899390	34900511

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 91.89.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1463 / max 59.0921, expressed in 461 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
56079	0.4991	183
56080	0.4947	263
56081	0.1525	67

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.89	gold quality
right testis	UBERON:0004534	91.76	gold quality
testis	UBERON:0000473	89.73	gold quality
sperm	CL:0000019	87.82	gold quality
right uterine tube	UBERON:0001302	86.98	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.77	gold quality
buccal mucosa cell	CL:0002336	78.11	silver quality
adrenal tissue	UBERON:0018303	77.30	gold quality
pituitary gland	UBERON:0000007	77.07	gold quality
adenohypophysis	UBERON:0002196	77.04	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.98	gold quality
tendon of biceps brachii	UBERON:0008188	75.18	gold quality
bronchial epithelial cell	CL:0002328	73.95	gold quality
adult organism	UBERON:0007023	73.24	gold quality
right adrenal gland	UBERON:0001233	73.23	gold quality
bronchus	UBERON:0002185	73.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	72.98	gold quality
left adrenal gland	UBERON:0001234	72.49	gold quality
left adrenal gland cortex	UBERON:0035825	72.19	gold quality
right adrenal gland cortex	UBERON:0035827	71.88	gold quality
spinal cord	UBERON:0002240	71.31	gold quality
adrenal cortex	UBERON:0001235	70.91	gold quality
adrenal gland	UBERON:0002369	70.78	gold quality
tendon	UBERON:0000043	70.36	gold quality
nasal cavity mucosa	UBERON:0001826	70.28	gold quality
fallopian tube	UBERON:0003889	69.42	gold quality
tibial nerve	UBERON:0001323	69.35	gold quality
corpus callosum	UBERON:0002336	68.90	gold quality
calcaneal tendon	UBERON:0003701	68.67	gold quality
secondary oocyte	CL:0000655	68.66	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.79
E-ENAD-17	no	40.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting TTC23L, 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-486-5P	99.51	70.39	707
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-12127	97.93	66.67	793
HSA-MIR-410-5P	96.55	66.28	459
HSA-MIR-323B-5P	96.12	66.39	472
HSA-MIR-494-5P	95.31	66.29	463

Literature-anchored findings (GeneRIF, showing 1)

• FLJ25439 is involved in pathways related to anti-apoptosis, protein folding, the cell cycle, and cytoskeleton regulation. (PMID:25751302)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ttc23l	ENSMUSG00000022249
rattus_norvegicus	Ttc23l	ENSRNOG00000055986

Paralogs (1): TTC23 (ENSG00000103852)

Protein

Protein identifiers

Tetratricopeptide repeat protein 23-like — Q6PF05 (reviewed: Q6PF05)

All UniProt accessions (5): A0A1W2PP54, A0A3B3IS63, A0A8V8TME1, D6RB54, Q6PF05

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Spindle. Midbody.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6PF05-1	1	yes
Q6PF05-2	2
Q6PF05-3	3

RefSeq proteins (6): NP_001304878, NP_001373098, NP_001373099, NP_001373100, NP_001373101, NP_653326* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR042621	TTC23/TTC23L	Family

UniProt features (17 total): sequence variant 6, sequence conflict 4, coiled-coil region 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PF05-F1	84.30	0.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 65 (showing top): GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOCC_MICROTUBULE_ORGANIZING_CENTER, TGTGTGA_MIR377, GOCC_CENTROSOME, WEBER_METHYLATED_IN_COLON_CANCER, GOCC_SPINDLE, GOCC_MIDBODY, GSE13522_WT_VS_IFNG_KO_SKIN_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_DN, HES4_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF30_TARGET_GENES, ZNF407_TARGET_GENES

GO Biological Process (1): response to endoplasmic reticulum stress (GO:0034976)

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

GO Cellular Component (5): centrosome (GO:0005813), spindle (GO:0005819), midbody (GO:0030496), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	2
cellular anatomical structure	2
cellular response to stress	1
binding	1
centriole	1
microtubule organizing center	1
microtubule cytoskeleton	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

232 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC23L	SPINK14	Q6IE38	506
TTC23L	RAI14	Q9P0K7	486
TTC23L	DTWD2	Q8NBA8	484
TTC23L	CFAP206	Q8IYR0	464
TTC23L	EIPR1	Q53HC9	460
TTC23L	ZBED5	Q49AG3	447
TTC23L	SLF2	Q8IX21	416
TTC23L	DNAJC21	Q5F1R6	397
TTC23L	BRIX1	Q8TDN6	394
TTC23L	VEZT	Q9HBM0	377
TTC23L	AGXT2	Q9BYV1	360
TTC23L	GARIN6	Q8NEG0	360
TTC23L	GRAMD1B	Q3KR37	359
TTC23L	NAALADL2	Q58DX5	338
TTC23L	CNRIP1	Q96F85	330

IntAct

86 interactions, top by confidence:

A	B	Type	Score
IQCE	TTC23L	psi-mi:“MI:0915”(physical association)	0.660
TTC23L	CCDC24	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	DNAAF11	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	ANKRD11	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	VPS9D1	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	DPF2	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	SPG21	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	AIRIM	psi-mi:“MI:0915”(physical association)	0.560
EFHC1	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
USP20	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	FAM161B	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	PICK1	psi-mi:“MI:0915”(physical association)	0.560
TSGA10IP	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	ZNF784	psi-mi:“MI:0915”(physical association)	0.560
MSGN1	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
GRIN2C	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	HRAS	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	HSPA5	psi-mi:“MI:0915”(physical association)	0.560
KLF11	TTC23L	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
TTC23L	COL26A1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (36): TTC23L (Two-hybrid), TTC23L (Two-hybrid), TTC23L (Two-hybrid), TTC23L (Two-hybrid), IQCE (Affinity Capture-MS), EFCAB7 (Affinity Capture-MS), VASP (Affinity Capture-MS), TTC23L (Two-hybrid), CTAGE5 (Two-hybrid), IQCE (Affinity Capture-MS), EFCAB7 (Affinity Capture-MS), VASP (Affinity Capture-MS), TTC23L (Two-hybrid), TTC23L (Two-hybrid), TTC23L (Two-hybrid)

ESM2 similar proteins: A0JM23, A0M8T3, A1X154, A4D7T3, A5A6J9, A6H6E9, A6H7D1, O14879, O75747, Q00PJ3, Q07DV3, Q07DX6, Q07DY6, Q07DZ7, Q07E17, Q07E43, Q09YH1, Q09YI3, Q09YJ5, Q09YK6, Q09YN0, Q14AT2, Q2IBB1, Q2IBB4, Q2IBE3, Q2IBF5, Q2IBG0, Q2KHY7, Q2QL84, Q2QLA4, Q2QLB5, Q2QLG0, Q32NR4, Q4R6M4, Q4V7F0, Q5R4M2, Q5W5X9, Q692V3, Q6AYP3, Q6P2S7

Diamond homologs: A6H6E9, A6H7D1, Q2KHY7, Q4V7F0, Q5W5X9, Q6PF05, Q8CHY7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2231 predictions. Top by Δscore:

Variant	Effect	Δscore
5:34839294:G:GT	donor_gain	1.0000
5:34839316:G:GT	donor_gain	1.0000
5:34866888:GCAG:G	acceptor_loss	1.0000
5:34866889:CA:C	acceptor_loss	1.0000
5:34866889:CAG:C	acceptor_gain	1.0000
5:34866890:A:AC	acceptor_loss	1.0000
5:34866890:A:AG	acceptor_gain	1.0000
5:34866890:AGA:A	acceptor_gain	1.0000
5:34866891:G:GG	acceptor_gain	1.0000
5:34866891:GA:G	acceptor_gain	1.0000
5:34866891:GAG:G	acceptor_gain	1.0000
5:34866891:GAGC:G	acceptor_gain	1.0000
5:34866891:GAGCC:G	acceptor_gain	1.0000
5:34867057:G:GG	donor_gain	1.0000
5:34867066:GCAG:G	donor_gain	1.0000
5:34867068:AG:A	donor_loss	1.0000
5:34867071:T:G	donor_loss	1.0000
5:34880305:ACAGG:A	donor_loss	1.0000
5:34880306:CAGG:C	donor_loss	1.0000
5:34880307:AGGT:A	donor_loss	1.0000
5:34880308:GGT:G	donor_loss	1.0000
5:34880309:GTAA:G	donor_loss	1.0000
5:34880310:T:G	donor_loss	1.0000
5:34839275:G:GT	donor_gain	0.9900
5:34839291:G:GT	donor_gain	0.9900
5:34839317:G:T	donor_gain	0.9900
5:34839538:G:GT	donor_gain	0.9900
5:34845599:GACT:G	donor_gain	0.9900
5:34845665:G:GT	donor_gain	0.9900
5:34845666:A:T	donor_gain	0.9900

AlphaMissense

2366 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:34862912:G:C	A132P	0.975
5:34862924:G:C	A136P	0.973
5:34864460:T:C	L187P	0.968
5:34867013:G:C	A262P	0.966
5:34864559:G:A	G220D	0.955
5:34867014:C:A	A262D	0.954
5:34880207:A:C	S326R	0.953
5:34880209:T:A	S326R	0.953
5:34880209:T:G	S326R	0.953
5:34850207:T:C	L93P	0.949
5:34868975:C:A	A304D	0.947
5:34880282:T:A	W351R	0.940
5:34880282:T:C	W351R	0.940
5:34862913:C:A	A132D	0.939
5:34863029:G:C	G171R	0.939
5:34868905:G:C	A281P	0.935
5:34863030:G:A	G171D	0.934
5:34867049:G:C	A274P	0.934
5:34862933:G:C	A139P	0.931
5:34850282:T:C	L118P	0.929
5:34850285:C:A	A119D	0.926
5:34866893:G:C	A222P	0.926
5:34868974:G:C	A304P	0.926
5:34862901:T:C	L128P	0.924
5:34866924:C:A	A232D	0.924
5:34850284:G:C	A119P	0.923
5:34880273:T:C	F348L	0.920
5:34880275:T:A	F348L	0.920
5:34880275:T:G	F348L	0.920
5:34862925:C:A	A136D	0.916

dbSNP variants (sampled 300 via entrez): RS1000138652 (5:34865420 T>A), RS1000142343 (5:34846278 A>G), RS1000154959 (5:34916318 G>A,C), RS1000205618 (5:34853552 G>T), RS1000258075 (5:34867327 T>A,G), RS1000277220 (5:34845989 C>T), RS1000383364 (5:34860394 A>G), RS1000450483 (5:34916667 A>C,T), RS1000454597 (5:34851818 G>T), RS1000467660 (5:34845018 G>A,C), RS1000491792 (5:34867744 T>C), RS1000494792 (5:34887158 C>T), RS1000533052 (5:34881162 G>A,C), RS1000556181 (5:34839052 G>A), RS1000601123 (5:34886494 C>A,T)

Disease associations

OMIM: gene MIM:616344 | disease phenotypes: MIM:614307

GenCC curated gene-disease

Mondo (1): alpha-methylacyl-CoA racemase deficiency (MONDO:0013681)

Orphanet (1): Congenital bile acid synthesis defect type 4 (Orphanet:79095)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002995_17	Dysphagia	8.000000e-06
GCST003518_4	Daytime sleep phenotypes	9.000000e-06
GCST009391_1923	Metabolite levels	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement
EFO:0010464	beta-aminoisobutyric acid measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C565768	Alpha-Methylacyl-CoA Racemase Deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases methylation	2
aristolochic acid I	increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
dimethylselenide	increases expression, increases oxidation	1
licochalcone B	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Tobacco Smoke Pollution	decreases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Hydroxyl Radical	increases expression, increases oxidation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01668186	Not specified	RECRUITING	Longitudinal Natural History Study of Patients With Peroxisome Biogenesis Disorders (PBD)