CDRT15

Summary

CDRT15 (CMT1A duplicated region transcript 15, HGNC:14395) is a protein-coding gene on chromosome 17p12, encoding CMT1A duplicated region transcript 15 protein (Q96T59).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 132 total — 88 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 3
• MANE Select transcript: NM_001007530

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14395
Approved symbol	CDRT15
Name	CMT1A duplicated region transcript 15
Location	17p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000223510
Ensembl biotype	protein_coding
Entrez	146822

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000420162, ENST00000431716

RefSeq mRNA: 2 — MANE Select: NM_001007530 NM_001007530, NM_001348781

CCDS: CCDS32569, CCDS86577

Canonical transcript exons

ENST00000420162 — 3 exons

Exon	Start	End
ENSE00001609434	14236572	14236862
ENSE00002425254	14236282	14236430
ENSE00003899504	14235673	14236011

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 82.14.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	82.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.05	silver quality
left testis	UBERON:0004533	80.26	gold quality
testis	UBERON:0000473	79.88	gold quality
granulocyte	CL:0000094	73.53	gold quality
lymph node	UBERON:0000029	69.47	gold quality
lower esophagus mucosa	UBERON:0035834	68.25	gold quality
mucosa of transverse colon	UBERON:0004991	67.57	gold quality
right lobe of liver	UBERON:0001114	65.49	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.53	gold quality
spleen	UBERON:0002106	63.95	gold quality
esophagus mucosa	UBERON:0002469	63.29	gold quality
apex of heart	UBERON:0002098	62.68	gold quality
small intestine Peyer’s patch	UBERON:0003454	61.57	gold quality
blood	UBERON:0000178	61.46	gold quality
skin of abdomen	UBERON:0001416	61.09	gold quality
rectum	UBERON:0001052	60.89	gold quality
small intestine	UBERON:0002108	60.59	gold quality
zone of skin	UBERON:0000014	59.90	gold quality
heart left ventricle	UBERON:0002084	59.51	gold quality
skin of leg	UBERON:0001511	59.20	gold quality
transverse colon	UBERON:0001157	59.01	gold quality
esophagus	UBERON:0001043	58.38	gold quality
right atrium auricular region	UBERON:0006631	58.34	gold quality
duodenum	UBERON:0002114	58.18	gold quality
fundus of stomach	UBERON:0001160	58.01	gold quality
monocyte	CL:0000576	57.97	gold quality
leukocyte	CL:0000738	57.88	gold quality
body of stomach	UBERON:0001161	57.61	gold quality
saliva-secreting gland	UBERON:0001044	57.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.54

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Bioinformatic analysis the expression and clinical significance of CDRT15 in cholangiocarcinoma using TCGA database. (PMID:37543771)

Cross-species orthologs

0 orthologs

Paralogs (1): CDRT15L2 (ENSG00000214819)

Protein

Protein identifiers

CMT1A duplicated region transcript 15 protein — Q96T59 (reviewed: Q96T59)

All UniProt accessions (2): Q96T59, F2Z3C1

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in fetal heart, kidney, liver, lung and spleen.

RefSeq proteins (2): NP_001007531, NP_001335710 (=MANE)

Domains & families (InterPro)

UniProt features (3 total): chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96T59-F1	52.21	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chr17p12, E2F3_UP.V1_UP, SRC_UP.V1_UP, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_12H_DN, GSE42724_NAIVE_VS_B1_BCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

114 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDRT15	TVP23B	Q9NYZ1	714
CDRT15	CDRT4	Q8N9R6	621
CDRT15	HS3ST3B1	Q9Y662	605
CDRT15	SMCO2	A6NFE2	600
CDRT15	TEKT3	Q9BXF9	580
CDRT15	TVP23C	Q96ET8	579
CDRT15	FBXW10B	O95170	576
CDRT15	A0A0A6YYB9	A0A0A6YYB9	574
CDRT15	ZNF18	P17022	507
CDRT15	ARHGAP44	Q17R89	418
CDRT15	MANSC4	A6NHS7	418
CDRT15	SHISA6	Q6ZSJ9	418
CDRT15	HS3ST3A1	Q9Y663	417
CDRT15	LSM2	Q9Y333	367
CDRT15	PPFIBP1	Q86W92	350

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CDRT15	CDRT15L2	psi-mi:“MI:0914”(association)	0.530
Dlg4	CDRT15	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (19): PMPCA (Affinity Capture-MS), PMPCB (Affinity Capture-MS), CDRT15L2 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), MAP4K5 (Affinity Capture-MS), NUDT8 (Affinity Capture-MS), DCAF11 (Affinity Capture-MS), IFI30 (Affinity Capture-MS), MAP4K5 (Affinity Capture-MS), CDRT15L2 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), NUDT8 (Affinity Capture-MS), NRD1 (Affinity Capture-MS), NUDT8 (Affinity Capture-MS), CDRT15L2 (Affinity Capture-MS)

ESM2 similar proteins: A1YEW3, A1YG31, A2T715, A2T7M0, A6NEV1, A6NGD5, A6NJL1, A6QPT6, A8MXV6, A8MZF0, A8WFF7, O08664, P03327, P06936, P0C6A0, P0DPQ3, P54257, P57086, P86478, P86479, P86480, P86481, P86496, Q13487, Q32PG5, Q505G4, Q5R7P6, Q68FX5, Q6J1H4, Q6NZN1, Q6ZMS7, Q6ZRT6, Q76NI1, Q7L3V2, Q7TPK6, Q7YR42, Q7Z6I6, Q80UE6, Q8IY33, Q8K2W9

Diamond homologs: A8MXV6, Q96T59

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	88
Likely pathogenic	4
Uncertain significance	35
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1047887	GRCh37/hg19 17p12(chr17:14100118-15455297)	Pathogenic
1180510	GRCh37/hg19 17p12(chr17:14098196-15442500)x3	Pathogenic
1328101	GRCh37/hg19 17p12(chr17:14073284-15442296)x3	Pathogenic
1330204	GRCh37/hg19 17p12(chr17:14096089-15492591)x3	Pathogenic
1460285	NC_000017.10:g.(?14139889)(15142928_?)del	Pathogenic
147669	GRCh38/hg38 17p12(chr17:14208455-15588434)x1	Pathogenic
148561	GRCh38/hg38 17p12(chr17:14208455-15538755)x3	Pathogenic
148562	GRCh38/hg38 17p12(chr17:14208455-15538755)x1	Pathogenic
149424	GRCh38/hg38 17p12(chr17:14208455-15579558)x1	Pathogenic
152376	GRCh38/hg38 17p12(chr17:14184616-15581044)x3	Pathogenic
152875	GRCh38/hg38 17p12(chr17:14186983-15570276)x3	Pathogenic
153240	GRCh38/hg38 17p12(chr17:14184616-15581544)x3	Pathogenic
153241	GRCh38/hg38 17p12(chr17:14184616-15581544)x1	Pathogenic
153289	GRCh38/hg38 17p12(chr17:14184616-15588218)x1	Pathogenic
154140	GRCh38/hg38 17p12(chr17:14179737-15571773)x1	Pathogenic
154234	GRCh38/hg38 17p12(chr17:14179737-15664355)x3	Pathogenic
154772	GRCh38/hg38 17p12(chr17:14208455-15579558)x3	Pathogenic
155232	GRCh38/hg38 17p12(chr17:14184470-15586786)x1	Pathogenic
155236	GRCh38/hg38 17p12(chr17:14184616-15597331)x3	Pathogenic
160871	GRCh38/hg38 17p12(chr17:14208455-15538752)x3	Pathogenic
1684556	GRCh37/hg19 17p12(chr17:14093318-15476314)x3	Pathogenic
1807700	GRCh37/hg19 17p12(chr17:14087934-15479940)x3	Pathogenic
1807743	GRCh37/hg19 17p12(chr17:14087934-15484630)x3	Pathogenic
1807816	GRCh37/hg19 17p12(chr17:14082945-15484858)x1	Pathogenic
1807821	GRCh37/hg19 17p12(chr17:14083055-15483608)x3	Pathogenic
1807927	GRCh37/hg19 17p12(chr17:14087788-15484858)x1	Pathogenic
1808529	GRCh37/hg19 17p12(chr17:14077819-15491532)x1	Pathogenic
1808605	GRCh37/hg19 17p12(chr17:14087934-15483608)x3	Pathogenic
1808614	GRCh37/hg19 17p12(chr17:14073563-15479923)x3	Pathogenic
1808665	GRCh37/hg19 17p12(chr17:14087934-15484358)x3	Pathogenic

SpliceAI

282 predictions. Top by Δscore:

Variant	Effect	Δscore
17:14236277:CGTG:C	donor_gain	1.0000
17:14236298:T:TA	donor_gain	0.9900
17:14236550:T:TA	donor_gain	0.9900
17:14236780:C:CA	donor_gain	0.9900
17:14236276:A:AC	donor_gain	0.9800
17:14236277:C:CC	donor_gain	0.9800
17:14236313:T:TA	donor_gain	0.9800
17:14236428:GAGCT:G	acceptor_gain	0.9700
17:14236429:AGCTG:A	acceptor_gain	0.9700
17:14236431:C:CC	acceptor_gain	0.9700
17:14236583:G:A	donor_gain	0.9700
17:14236709:A:AC	donor_gain	0.9600
17:14236278:G:C	donor_gain	0.9500
17:14236328:C:CA	donor_gain	0.9500
17:14236430:GCTGA:G	acceptor_gain	0.9500
17:14236269:C:CT	donor_gain	0.9400
17:14236270:T:TT	donor_gain	0.9400
17:14236272:CA:C	donor_gain	0.9400
17:14236273:A:AC	donor_gain	0.9400
17:14236529:A:AC	donor_gain	0.9400
17:14236563:C:CT	donor_gain	0.9400
17:14236564:C:CT	donor_gain	0.9400
17:14236570:A:AC	donor_gain	0.9400
17:14236571:C:CC	donor_gain	0.9400
17:14236777:ACTC:A	donor_gain	0.9400
17:14236778:CTCC:C	donor_gain	0.9400
17:14236009:CTC:C	acceptor_gain	0.9300
17:14236225:T:TA	donor_gain	0.9300
17:14236295:AGCT:A	donor_gain	0.9300
17:14236427:GGAG:G	acceptor_gain	0.9300

AlphaMissense

1190 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:14236828:G:C	F2L	0.954
17:14236828:G:T	F2L	0.954
17:14236830:A:G	F2L	0.954
17:14236792:G:C	F14L	0.952
17:14236792:G:T	F14L	0.952
17:14236794:A:G	F14L	0.952
17:14236765:G:C	F23L	0.939
17:14236765:G:T	F23L	0.939
17:14236767:A:G	F23L	0.939
17:14235889:A:C	F178L	0.912
17:14235889:A:T	F178L	0.912
17:14235891:A:G	F178L	0.912
17:14236816:G:C	F6L	0.868
17:14236816:G:T	F6L	0.868
17:14236818:A:G	F6L	0.868
17:14236829:A:C	F2C	0.847
17:14236742:A:G	I31T	0.839
17:14236793:A:G	F14S	0.832
17:14236793:A:C	F14C	0.805
17:14236771:G:C	S21R	0.804
17:14236771:G:T	S21R	0.804
17:14236773:T:G	S21R	0.804
17:14236766:A:C	F23C	0.798
17:14236829:A:G	F2S	0.796
17:14236789:C:A	R15S	0.775
17:14236789:C:G	R15S	0.775
17:14236766:A:G	F23S	0.757
17:14236817:A:C	F6C	0.739
17:14236817:A:G	F6S	0.735
17:14235991:T:A	K144N	0.731

dbSNP variants (sampled 300 via entrez): RS1000770942 (17:14238519 C>T), RS1001931217 (17:14237167 G>T), RS1003185480 (17:14235395 A>G), RS1010250446 (17:14237242 G>C), RS1019309034 (17:14238768 C>G,T), RS1020291586 (17:14238481 C>G,T), RS1028684302 (17:14235567 G>A,C,T), RS1029269403 (17:14238529 C>T), RS1035761584 (17:14237169 C>G), RS1036757189 (17:14237359 T>A), RS1036852310 (17:14237109 G>A), RS1038441082 (17:14235172 C>T), RS1048339652 (17:14237496 T>A), RS1053274916 (17:14236501 A>G), RS1057075329 (17:14238446 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:118220, MIM:162500, MIM:118300, MIM:181500, MIM:209850

GenCC curated gene-disease

Mondo (9): scoliosis (MONDO:0005392), Charcot-Marie-Tooth disease type 1A (MONDO:0007309), Charcot-Marie-Tooth disease type 1 (MONDO:0019011), primary ovarian failure (MONDO:0005387), autism spectrum disorder (MONDO:0005258), hereditary neuropathy with liability to pressure palsies (MONDO:0008087), Charcot-Marie-Tooth disease type 1E (MONDO:0007311), schizophrenia (MONDO:0005090), autism (MONDO:0005260)

Orphanet (7): Charcot-Marie-Tooth disease type 1A (Orphanet:101081), Charcot-Marie-Tooth disease type 1 (Orphanet:65753), Hereditary neuropathy with liability to pressure palsies (Orphanet:640), Charcot-Marie-Tooth disease type 1E (Orphanet:90658), NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

3 total (3 of 3 shown, HPO-id order):

HPO	Term
HP:0002650	Scoliosis
HP:0100753	Schizophrenia
HP:0000717	Autism

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST006291_38	Spherical equivalent or myopia (age of diagnosis)	3.000000e-12
GCST009391_1186	Metabolite levels	2.000000e-06
GCST010002_121	Refractive error	4.000000e-27

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset
EFO:0021575	adipic acid measurement

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D016649	Primary Ovarian Insufficiency	C12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750
D012600	Scoliosis	C05.116.900.800.875
C537986	Charcot-Marie-Tooth disease, Type 1E (supp.)
C536965	Tomaculous neuropathy (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Arsenic	affects methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00508066	PHASE4	COMPLETED	Continuous Local Infusion of Anesthetic at the Incisional Site for Scoliosis Surgery
NCT00510575	PHASE4	COMPLETED	Surgical Outcomes Using Variable Rod Diameters in the Treatment of Idiopathic Scoliosis
NCT00768313	PHASE4	WITHDRAWN	Phase IV Comparing Rods of Yield Strengths to Correct Adolescent Idiopathic Scoliosis.
NCT00880607	PHASE4	COMPLETED	Intrathecal Morphine Versus Epidural Extended Release Morphine for Pediatric Patients Undergoing Spinal Fusion
NCT00958581	PHASE4	COMPLETED	Tranexamic Acid (TXA) Versus Epsilon Aminocaproic Acid (EACA) Versus Placebo for Spine Surgery
NCT01852747	PHASE4	TERMINATED	Comparison of Actifuse ABX and Local Bone in Spinal Surgery
NCT02464813	PHASE4	COMPLETED	Effect of Pregabalin on Immediate Post-operative and Longterm Pain
NCT02465099	PHASE4	TERMINATED	Posterior Spinal Fusion With Two Energy Dissection Techniques
NCT06540885	PHASE4	RECRUITING	A Comparison Between Palonosetron Versus Granisetron as PONV Prophylaxis in Scoliotic Patients Undergoing Spine Surgery
NCT06616220	PHASE4	COMPLETED	Dexamethasone for ESPB in Pain Management After Pediatric Idiopathic Scoliosis Surgery
NCT06789016	PHASE4	COMPLETED	Dexmedetomidine for ESPB in Pain Management After Pediatric Idiopathic Scoliosis Surgery
NCT00417066	PHASE4	COMPLETED	Flexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693	PHASE4	COMPLETED	Evaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616	PHASE4	COMPLETED	Estrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501	PHASE4	UNKNOWN	Effects of ADSC Therapy in Women With POF
NCT02783937	PHASE4	COMPLETED	Filgrastim for Premature Ovarian Insufficiency
NCT03535480	PHASE4	UNKNOWN	Autologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT00323752	PHASE3	COMPLETED	Recombinant Human Erythropoietin Compared to Autologous Pre-Donation Prior to Scoliosis Surgery in Children.
NCT00684112	PHASE3	COMPLETED	Analgesic Effects of Gabapentin After Scoliosis Surgery in Children
NCT00737997	PHASE3	COMPLETED	Effect of Early Morphine Administration on the Development of Acute Opioid Tolerance During Pediatric Scoliosis Surgery
NCT01103115	PHASE3	COMPLETED	Calcium + Vitamin D Supplementation for Low Bone Mass in Adolescent Idiopathic Scoliosis (AIS)
NCT01108211	PHASE3	COMPLETED	Improving Low Bone Mass With Vibration Therapy in Adolescent Idiopathic Scoliosis (AIS)
NCT01205256	PHASE3	COMPLETED	IRB-HSR# 14145 R,S Methadone: Analgesia and Pharmacokinetics in Adolescents Undergoing Scoliosis Correction
NCT02558010	PHASE3	COMPLETED	Perioperative Methadone Use to Decrease Opioid Requirement in Pediatric Spinal Fusion Patients
NCT03537612	PHASE3	TERMINATED	Sensorial and Physiological Mechanism-based Assessments of Perioperative Pain
NCT02579759	PHASE3	COMPLETED	Phase III Trial Assessing the Efficacy and Safety of PXT3003 in CMT1A Patients (PLEO-CMT)
NCT00140998	PHASE3	COMPLETED	Estrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00273598	PHASE2	COMPLETED	Comparing Two Instrumentation Systems for the Treatment of Adolescent Scoliosis
NCT01148888	PHASE2	COMPLETED	The Effect of Magnesium Sulfate on Motor and Somatosensory Evoked Potentials in Children Undergoing Scoliosis Surgery
NCT02600286	PHASE2	TERMINATED	Ulipristal Acetate In Disease Charcot-Marie-Tooth Type of 1A
NCT02967679	PHASE2	COMPLETED	SERENDEM : MD1003 in Patients Suffering From Demyelinating Neuropathies, an Open Label Pilot Study
NCT00001951	PHASE2	COMPLETED	Hormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019	PHASE2	WITHDRAWN	Effects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494	PHASE2	COMPLETED	GnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients