LINC01976

long intergenic non-protein coding RNA 1976, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 17:43926845-43950464

Links

ENSG00000261514 ∙ NCBI:107546764 ∙ ∙ HGNC:52803 ∙ ∙ ∙ 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 LINC01976 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01976 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 LINC01976

This is a list of pathogenic ClinVar variants found in the LINC01976 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43941176-G-A		not specified	Likely benign (Aug 02, 2021)
17-43941197-T-A		not specified	Uncertain significance (Jan 30, 2024)
17-43941213-A-T		not specified	Uncertain significance (Dec 20, 2023)
17-43941470-C-A		not specified	Uncertain significance (Mar 24, 2023)
17-43941528-G-A		not specified	Uncertain significance (Aug 30, 2021)
17-43941606-C-T		not specified	Uncertain significance (Mar 20, 2023)
17-43941641-C-T		not specified	Uncertain significance (Aug 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC01976	protein_coding	protein_coding	ENST00000565120	2	597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0116	0.421	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	22	34.1	0.645	0.00000214	392
Missense in Polyphen		2	1.1781	1.6977		14
Synonymous	1.56	9	17.2	0.522	0.00000130	128
Loss of Function	-1.29	2	0.775	2.58	3.27e-8	11

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