CDRT15L2

CMT1A duplicated region transcript 15 like 2

Basic information

Region (hg38): 17:20579724-20580911

Links

ENSG00000214819 ∙ NCBI:256223 ∙ ∙ HGNC:34075 ∙ Uniprot:A8MXV6 ∙ 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 CDRT15L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDRT15L2 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				1		1
missense			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in CDRT15L2

This is a list of pathogenic ClinVar variants found in the CDRT15L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-20579747-T-C		not specified	Uncertain significance (Jul 20, 2022)
17-20579754-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-20579850-G-T		not specified	Uncertain significance (Jul 20, 2022)
17-20579859-C-T		not specified	Uncertain significance (Jan 17, 2025)
17-20579868-G-C		not specified	Uncertain significance (Jan 19, 2022)
17-20579877-C-T		not specified	Uncertain significance (Dec 17, 2024)
17-20579894-A-G		not specified	Uncertain significance (Jul 10, 2024)
17-20579954-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-20579981-C-T		not specified	Uncertain significance (Jan 16, 2025)
17-20579988-C-G		not specified	Uncertain significance (Sep 30, 2024)
17-20580155-G-T		not specified	Uncertain significance (Jan 18, 2023)
17-20580157-C-T		not specified	Uncertain significance (Sep 04, 2024)
17-20580170-T-G		not specified	Uncertain significance (Mar 29, 2024)
17-20580182-C-T		not specified	Uncertain significance (Sep 27, 2021)
17-20580188-C-T		not specified	Uncertain significance (Jan 03, 2025)
17-20580193-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-20580227-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-20580233-G-A		not specified	Uncertain significance (Feb 18, 2025)
17-20580236-C-A		not specified	Uncertain significance (Apr 07, 2022)
17-20580241-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-20580244-G-A		not specified	Uncertain significance (Jul 19, 2022)
17-20580244-G-T		not specified	Uncertain significance (Feb 27, 2024)
17-20580267-C-A		not specified	Uncertain significance (Apr 18, 2023)
17-20580287-C-T		not specified	Uncertain significance (Aug 14, 2024)
17-20580332-C-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDRT15L2	protein_coding	protein_coding	ENST00000399044	2	1188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00177	0.492	125137	0	16	125153	0.0000639

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.154	129	134	0.962	0.00000734	1751
Missense in Polyphen		37	39.046	0.9476		569
Synonymous	-0.710	59	52.5	1.12	0.00000281	623
Loss of Function	0.0673	4	4.15	0.964	3.39e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000266
Middle Eastern	0.000110	0.000109
South Asian	0.000310	0.000294
Other	0.000168	0.000164

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0304

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane