LINC02166

long intergenic non-protein coding RNA 2166, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 16:89682506-89686921

Links

ENSG00000260259 ∙ NCBI:105371416 ∙ ∙ HGNC:53027 ∙ ∙ ∙ 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 LINC02166 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC02166 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 LINC02166

This is a list of pathogenic ClinVar variants found in the LINC02166 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89686715-C-T		Inborn genetic diseases	Uncertain significance (Jun 02, 2024)
16-89686720-C-G			Likely benign (Aug 01, 2024)
16-89686722-A-T			Likely benign (Aug 01, 2024)
16-89686734-C-A		Al Kaissi syndrome	Pathogenic/Likely pathogenic (-)
16-89686735-G-C		Al Kaissi syndrome • Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
16-89686747-C-A		Inborn genetic diseases	Uncertain significance (May 30, 2022)
16-89686751-A-G		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
16-89686761-T-G		Al Kaissi syndrome	Conflicting classifications of pathogenicity (Jun 01, 2022)
16-89686796-G-A		Inborn genetic diseases	Uncertain significance (May 10, 2021)
16-89686802-G-A		Al Kaissi syndrome	Pathogenic (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC02166	protein_coding	protein_coding	ENST00000567544	2	3950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000318	0.375	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.354	100	90.5	1.10	0.00000619	819
Missense in Polyphen
Synonymous	0.251	38	40.0	0.950	0.00000283	289
Loss of Function	-0.133	5	4.69	1.07	3.52e-7	34

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

Haploinsufficiency Scores

• ghis: 0.436