TTC24

Summary

TTC24 (tetratricopeptide repeat domain 24, HGNC:32348) is a protein-coding gene on chromosome 1q22, encoding Tetratricopeptide repeat protein 24 (A2A3L6).

At a glance

• Clinical variants (ClinVar): 92 total
• MANE Select transcript: NM_001105669

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32348
Approved symbol	TTC24
Name	tetratricopeptide repeat domain 24
Location	1q22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187862
Ensembl biotype	protein_coding
Entrez	164118

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 retained_intron, 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000368236, ENST00000413282, ENST00000462049, ENST00000478081, ENST00000495690

RefSeq mRNA: 1 — MANE Select: NM_001105669 NM_001105669

CCDS: CCDS53379

Canonical transcript exons

ENST00000368236 — 11 exons

Exon	Start	End
ENSE00001446662	156586469	156587719
ENSE00002246691	156579723	156579758
ENSE00002298601	156581361	156582070
ENSE00002304117	156585949	156586045
ENSE00002312153	156585125	156585231
ENSE00003481568	156583338	156583450
ENSE00003525724	156583797	156583895
ENSE00003604126	156584877	156584974
ENSE00003642703	156585713	156585826
ENSE00003706306	156582231	156582434
ENSE00003707652	156583042	156583170

Expression profiles

Bgee: expression breadth ubiquitous, 107 present calls, max score 79.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3462 / max 36.6681, expressed in 83 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5732	0.3379	81
201756	0.0083	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	79.10	gold quality
lymph node	UBERON:0000029	78.56	gold quality
spleen	UBERON:0002106	74.18	gold quality
vermiform appendix	UBERON:0001154	73.57	gold quality
blood	UBERON:0000178	65.71	gold quality
bone marrow	UBERON:0002371	65.31	gold quality
tonsil	UBERON:0002372	64.23	gold quality
leukocyte	CL:0000738	63.45	gold quality
monocyte	CL:0000576	62.95	gold quality
bone marrow cell	CL:0002092	60.16	silver quality
small intestine Peyer’s patch	UBERON:0003454	57.39	gold quality
pituitary gland	UBERON:0000007	56.71	gold quality
adenohypophysis	UBERON:0002196	56.39	gold quality
small intestine	UBERON:0002108	55.75	gold quality
primary visual cortex	UBERON:0002436	55.38	gold quality
gastrocnemius	UBERON:0001388	54.18	gold quality
lower esophagus mucosa	UBERON:0035834	53.99	gold quality
muscle of leg	UBERON:0001383	53.59	gold quality
mucosa of transverse colon	UBERON:0004991	53.17	gold quality
gall bladder	UBERON:0002110	52.10	gold quality
skeletal muscle tissue	UBERON:0001134	52.06	gold quality
muscle tissue	UBERON:0002385	49.02	gold quality
superior frontal gyrus	UBERON:0002661	48.58	gold quality
hindlimb stylopod muscle	UBERON:0004252	47.35	silver quality
Brodmann (1909) area 9	UBERON:0013540	46.66	gold quality
right coronary artery	UBERON:0001625	46.10	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	46.05	gold quality
frontal cortex	UBERON:0001870	45.95	gold quality
right frontal lobe	UBERON:0002810	45.83	gold quality
body of stomach	UBERON:0001161	45.79	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting TTC24, 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-4721	99.26	66.05	818
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-647	97.73	67.79	927
HSA-MIR-12128	96.67	66.98	1471
HSA-MIR-764	94.16	64.85	656

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Ttc24	ENSRNOG00000028765

Paralogs (6): TTC28 (ENSG00000100154), GPSM2 (ENSG00000121957), TTC29 (ENSG00000137473), GPSM1 (ENSG00000160360), RAPSN (ENSG00000165917), GPSM3 (ENSG00000213654)

Protein

Protein identifiers

Tetratricopeptide repeat protein 24 — A2A3L6 (reviewed: A2A3L6)

All UniProt accessions (1): A2A3L6

RefSeq proteins (1): NP_001099139* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR019734	TPR_rpt	Repeat
IPR024812	TPR_24	Family

Pfam: PF13176, PF13424

UniProt features (17 total): repeat 8, region of interest 3, sequence variant 3, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2A3L6-F1	73.99	0.56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): chr1q22, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GSE13522_WT_VS_IFNG_KO_SKIN_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, NFKBIA_TARGET_GENES, NKX2_3_TARGET_GENES, SFMBT1_TARGET_GENES, SIX1_TARGET_GENES, ZNF528_TARGET_GENES, MIR6814_5P, GSE10211_UV_INACT_SENDAI_VS_LIVE_SENDAI_VIRUS_TRACHEAL_EPITHELIAL_CELLS_DN, DESCARTES_FETAL_PANCREAS_LYMPHOID_CELLS, ZNF134_TARGET_GENES, HOEK_NK_CELL_2011_2012_TIV_1D_VS_0DY_ADULT_1D_DN

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

978 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TTC24	GON4L	Q3T8J9	567
TTC24	IQGAP3	Q86VI3	440
TTC24	NANS	Q9NR45	438
TTC24	ITPRIPL2	Q3MIP1	403
TTC24	CYTH2	Q99418	393
TTC24	SPTA1	P02549	373
TTC24	ASH1L	Q9NR48	359
TTC24	BCAN	Q96GW7	325
TTC24	PPP1R16A	Q96I34	318
TTC24	MEF2D	Q14814	283
TTC24	IFT38	Q96AJ1	283
TTC24	COG2	Q14746	250
TTC24	KIFAP3	Q92845	222
TTC24	MYL6B	P14649	210
TTC24	IST1	P53990	206

IntAct

82 interactions, top by confidence:

A	B	Type	Score
TTC24	LNX2	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	RADIL	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	HTRA1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	RHPN1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	HTRA4	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	APBA1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	GORASP1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
LNX1	TTC24	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	PATJ	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	TAMALIN	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	GORASP2	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	ARHGEF12	psi-mi:“MI:0407”(direct interaction)	0.440
TTC24	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (1): NUP98 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1L3T7, A2A3L6, A4IFI1, A7E3N7, A8MYJ7, A8VU90, O94761, O94812, O95153, O95382, P97680, Q0P5G1, Q13671, Q14154, Q3UYR4, Q4V896, Q53GL7, Q569K6, Q58CQ5, Q58EX7, Q66H85, Q6DT37, Q6F5E8, Q6ZVH7, Q76MJ5, Q7TNF8, Q7Z3H0, Q80UU1, Q80UW5, Q8BWA8, Q8BXP5, Q8BYG0, Q8CIE4, Q8CJ00, Q8IYJ3, Q8NAG6, Q8TE82, Q91WA6, Q91WE1, Q921Q7

Diamond homologs: A2A3L6, Q8BYG0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Ras activation upon Ca2+ influx through NMDA receptor	5	66.4×	4e-07
Unblocking of NMDA receptors, glutamate binding and activation	5	63.2×	4e-07
Negative regulation of NMDA receptor-mediated neuronal transmission	5	63.2×	4e-07
Long-term potentiation	5	55.3×	7e-07
Assembly and cell surface presentation of NMDA receptors	8	47.2×	7e-10
Neurexins and neuroligins	8	36.6×	3e-09
Protein-protein interactions at synapses	5	30.9×	1e-05
RHOA GTPase cycle	5	8.7×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	101.5×	1e-17
protein localization to synapse	6	73.0×	2e-08
receptor clustering	7	69.3×	1e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	55.1×	5e-09
regulation of small GTPase mediated signal transduction	5	11.4×	3e-03
cell-cell adhesion	7	11.3×	2e-04
protein-containing complex assembly	6	10.8×	7e-04
chemical synaptic transmission	6	7.4×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	81
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1628 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156579759:GTAAG:G	donor_loss	1.0000
1:156582395:G:GT	donor_gain	1.0000
1:156582403:G:GT	donor_gain	1.0000
1:156583169:TGG:T	donor_loss	1.0000
1:156583171:G:GG	donor_gain	1.0000
1:156583171:GTA:G	donor_loss	1.0000
1:156583172:T:G	donor_loss	1.0000
1:156583795:A:AG	acceptor_gain	1.0000
1:156583796:G:GG	acceptor_gain	1.0000
1:156584947:G:GT	donor_gain	1.0000
1:156585228:GAGC:G	donor_gain	1.0000
1:156585230:GC:G	donor_gain	1.0000
1:156579755:GGAG:G	donor_gain	0.9900
1:156579756:GAG:G	donor_gain	0.9900
1:156579756:GAGG:G	donor_gain	0.9900
1:156579759:G:GG	donor_gain	0.9900
1:156579760:T:G	donor_loss	0.9900
1:156581359:A:AG	acceptor_gain	0.9900
1:156581360:G:GG	acceptor_gain	0.9900
1:156581360:GCCCT:G	acceptor_gain	0.9900
1:156581969:G:GT	donor_gain	0.9900
1:156582089:G:T	donor_gain	0.9900
1:156582226:TCTA:T	acceptor_loss	0.9900
1:156582227:CTA:C	acceptor_loss	0.9900
1:156582228:TAG:T	acceptor_loss	0.9900
1:156582229:A:AC	acceptor_loss	0.9900
1:156582433:CG:C	donor_gain	0.9900
1:156582434:GG:G	donor_gain	0.9900
1:156582435:G:GG	donor_gain	0.9900
1:156582435:GT:G	donor_loss	0.9900

AlphaMissense

3748 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156583074:A:C	S315R	0.988
1:156583076:C:A	S315R	0.988
1:156583076:C:G	S315R	0.988
1:156583376:G:T	G360W	0.981
1:156583377:G:A	G360E	0.977
1:156583433:G:C	A379P	0.973
1:156582362:G:T	G280W	0.972
1:156583376:G:A	G360R	0.970
1:156583376:G:C	G360R	0.970
1:156583146:G:C	A339P	0.969
1:156583092:T:C	F321L	0.965
1:156583094:T:A	F321L	0.965
1:156583094:T:G	F321L	0.965
1:156583125:G:C	A332P	0.962
1:156583090:C:A	A320D	0.959
1:156582363:G:A	G280E	0.957
1:156582362:G:A	G280R	0.956
1:156582362:G:C	G280R	0.956
1:156583101:A:C	S324R	0.956
1:156583103:C:A	S324R	0.956
1:156583103:C:G	S324R	0.956
1:156582419:G:C	A299P	0.955
1:156583385:G:C	A363P	0.955
1:156582308:G:C	A262P	0.954
1:156582422:G:C	A300P	0.952
1:156581725:T:C	F121L	0.951
1:156581727:C:A	F121L	0.951
1:156581727:C:G	F121L	0.951
1:156582299:T:C	F259L	0.951
1:156582301:C:A	F259L	0.951

dbSNP variants (sampled 300 via entrez): RS1000108023 (1:156585585 C>T), RS1000164853 (1:156580836 A>G), RS1000661597 (1:156585496 C>T), RS1000977216 (1:156584025 G>C), RS1001109875 (1:156584293 G>C), RS1001893246 (1:156580528 A>G), RS1001915228 (1:156584759 C>T), RS1002496196 (1:156578806 C>T), RS1002530248 (1:156587287 G>A), RS1002648030 (1:156582410 C>T), RS1002700442 (1:156582616 T>G), RS1003435601 (1:156581303 C>T), RS1003592639 (1:156585952 C>T), RS1003953753 (1:156587439 G>A), RS1004006646 (1:156581996 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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
Benzo(a)pyrene	decreases methylation	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	decreases methylation	1
Vitamin E	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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