LINC02456

long intergenic non-protein coding RNA 2456, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 12:102257213-102463502

Links

ENSG00000283052 ∙ NCBI:105369942 ∙ ∙ HGNC:53389 ∙ ∙ ∙ 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 LINC02456 gene.

• Growth delay due to insulin-like growth factor type 1 deficiency (140 variants)
• not provided (27 variants)
• Inborn genetic diseases (3 variants)
• Intellectual disability (1 variants)
• not specified (1 variants)
• IGF1-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 LINC02456 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		1	115	23	24	163
Total	0	1	115	23	24

Variants in LINC02456

This is a list of pathogenic ClinVar variants found in the LINC02456 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-102395885-T-C		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102395909-A-G		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102395924-T-C		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396014-AGTC-TATTCAATTAGTTACATTTTAG		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jun 14, 2016)
12-102396074-C-G		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 12, 2018)
12-102396123-G-A		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 13, 2018)
12-102396196-A-G		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 12, 2018)
12-102396264-T-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396280-C-G		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396326-A-G		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102396388-C-T		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396414-C-T		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 12, 2018)
12-102396516-G-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102396577-T-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102396663-T-G		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396788-C-CT		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jun 14, 2016)
12-102396837-G-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102396969-G-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102396974-G-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102397002-A-T		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 12, 2018)
12-102397058-C-T		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102397175-C-A		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 13, 2018)
12-102397175-C-T		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102397218-A-T		Growth delay due to insulin-like growth factor type 1 deficiency	Uncertain significance (Jan 12, 2018)
12-102397237-A-C		Growth delay due to insulin-like growth factor type 1 deficiency	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP