LINC02245

long intergenic non-protein coding RNA 2245, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 2:64901840-65056233

Links

ENSG00000237638 ∙ NCBI:400958 ∙ ∙ HGNC:53134 ∙ ∙ ∙ 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 LINC02245 gene.

• not provided (163 variants)
• Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome (24 variants)
• Inborn genetic diseases (15 variants)
• not specified (6 variants)
• SLC1A4-related condition (1 variants)
• Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC02245 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	9	7	81	64	29	190
Total	9	7	81	64	29

Highest pathogenic variant AF is 0.000105

Variants in LINC02245

This is a list of pathogenic ClinVar variants found in the LINC02245 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-64989247-TC-T			Benign (May 15, 2021)
2-64989251-GGCGGCGGCTCCC-G			Benign (May 14, 2021)
2-64989311-C-G			Benign (May 20, 2021)
2-64989353-T-C			Benign (May 14, 2021)
2-64989513-C-G			Benign (May 14, 2021)
2-64989514-G-C			Benign (May 14, 2021)
2-64989609-C-T			Benign (May 16, 2021)
2-64989643-C-T			Uncertain significance (Dec 01, 2018)
2-64989645-T-C		Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome	Pathogenic (Mar 01, 2023)
2-64989664-C-A			Benign (Jan 31, 2024)
2-64989679-C-T			Likely benign (Jan 20, 2024)
2-64989683-G-A			Benign/Likely benign (Jul 01, 2024)
2-64989685-T-C		SLC1A4-related disorder	Likely benign (Jan 23, 2023)
2-64989691-G-A			Likely benign (Jun 01, 2024)
2-64989691-G-T			Likely benign (Dec 30, 2023)
2-64989692-G-A			Uncertain significance (May 12, 2022)
2-64989694-G-A			Likely benign (Jan 19, 2024)
2-64989694-G-T			Likely benign (Jan 05, 2023)
2-64989703-C-A			Likely benign (Feb 09, 2023)
2-64989703-C-T			Likely benign (Oct 14, 2023)
2-64989706-G-C			Likely benign (Sep 28, 2023)
2-64989708-C-A			Uncertain significance (Feb 19, 2022)
2-64989708-C-T		SLC1A4-related disorder	Conflicting classifications of pathogenicity (Jan 31, 2024)
2-64989709-C-T			Likely benign (Nov 06, 2023)
2-64989711-G-A			Uncertain significance (Aug 09, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP