LINC02583

long intergenic non-protein coding RNA 2583, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 2:46429090-46528299

Links

ENSG00000187600 ∙ NCBI:101805491 ∙ ∙ HGNC:53812 ∙ ∙ ∙ 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 LINC02583 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC02583 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						0
Total	0	0	0	0	0

Variants in LINC02583

This is a list of pathogenic ClinVar variants found in the LINC02583 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-46479589-G-T		not specified	Uncertain significance (Dec 20, 2023)
2-46479620-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-46479631-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-46479657-G-T		not specified	Uncertain significance (Oct 06, 2021)
2-46480456-G-C		not specified	Uncertain significance (Nov 22, 2021)
2-46480477-T-C		not specified	Uncertain significance (Mar 28, 2022)
2-46480487-C-T		not specified	Uncertain significance (Jun 17, 2022)
2-46480517-G-A		not specified	Uncertain significance (Oct 18, 2021)
2-46480553-C-T		not specified	Likely benign (Sep 26, 2023)
2-46480562-T-C		not specified	Uncertain significance (Mar 07, 2024)
2-46480599-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-46480613-T-A		not specified	Uncertain significance (Aug 02, 2023)
2-46480615-C-T		not specified	Uncertain significance (Mar 29, 2023)
2-46480622-A-C		not specified	Uncertain significance (Aug 04, 2023)
2-46480627-G-A		not specified	Uncertain significance (May 03, 2023)
2-46480688-T-C			Likely benign (Mar 01, 2023)
2-46480759-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-46512063-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-46512074-A-G		not specified	Uncertain significance (Nov 19, 2022)
2-46512140-T-G		not specified	Uncertain significance (Jul 05, 2023)
2-46512244-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-46512308-C-T		not specified	Uncertain significance (Jun 09, 2022)
2-46512321-C-T		not specified	Uncertain significance (May 26, 2023)
2-46512347-T-C		not specified	Uncertain significance (May 03, 2023)
2-46512452-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC02583	protein_coding	protein_coding	ENST00000434431	3	55236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000361	0.384	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.216	140	133	1.05	0.00000840	1423
Missense in Polyphen		46	46.491	0.98944		531
Synonymous	1.65	39	54.5	0.716	0.00000353	416
Loss of Function	0.209	7	7.62	0.918	3.23e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP