CDRT15

CMT1A duplicated region transcript 15

Basic information

Region (hg38): 17:14235673-14236862

Links

ENSG00000223510 ∙ NCBI:146822 ∙ ∙ HGNC:14395 ∙ Uniprot:Q96T59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDRT15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDRT15 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	16	0	0

Variants in CDRT15

This is a list of pathogenic ClinVar variants found in the CDRT15 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-14235936-G-A		not specified	Uncertain significance (Oct 20, 2021)
17-14236001-T-C		not specified	Uncertain significance (Jun 07, 2023)
17-14236004-G-A		not specified	Uncertain significance (Dec 04, 2023)
17-14236355-G-T		not specified	Uncertain significance (Jun 24, 2022)
17-14236388-G-A		not specified	Uncertain significance (Jan 31, 2023)
17-14236419-A-G		not specified	Uncertain significance (Oct 06, 2021)
17-14236422-G-C		not specified	Uncertain significance (Nov 17, 2022)
17-14236575-G-A		not specified	Uncertain significance (Jun 02, 2024)
17-14236589-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-14236635-C-T		not specified	Uncertain significance (Feb 10, 2023)
17-14236662-C-T		not specified	Uncertain significance (Jun 07, 2024)
17-14236721-G-A		not specified	Uncertain significance (Jul 20, 2021)
17-14236778-C-T		not specified	Uncertain significance (Oct 28, 2023)
17-14236785-C-T		not specified	Uncertain significance (Mar 28, 2024)
17-14236791-T-C		not specified	Uncertain significance (Apr 08, 2024)
17-14236815-G-A		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDRT15	protein_coding	protein_coding	ENST00000420162	3	1190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000128	0.120	117722	0	7827	125549	0.0317

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.567	111	95.4	1.16	0.00000508	1150
Missense in Polyphen		36	32.256	1.1161		414
Synonymous	-0.253	44	41.9	1.05	0.00000256	404
Loss of Function	-0.660	8	6.22	1.29	4.50e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0703	0.0617
Ashkenazi Jewish	0.0275	0.0237
East Asian	0.128	0.0925
Finnish	0.0362	0.0283
European (Non-Finnish)	0.0323	0.0262
Middle Eastern	0.128	0.0925
South Asian	0.0337	0.0290
Other	0.0426	0.0359

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0270

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.187
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0262

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium