LINC01118

long intergenic non-protein coding RNA 1118, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 2:46698940-46913231

Links

ENSG00000222005 ∙ NCBI:388948 ∙ ∙ HGNC:49261 ∙ ∙ ∙ 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 LINC01118 gene.

• Inborn genetic diseases (28 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01118 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			25	3	3	31
Total	0	0	25	3	3

Variants in LINC01118

This is a list of pathogenic ClinVar variants found in the LINC01118 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-46758547-A-G		not specified	Uncertain significance (Apr 07, 2022)
2-46758586-T-A		not specified	Uncertain significance (Jun 26, 2023)
2-46758587-C-T			Benign (May 31, 2018)
2-46758588-G-A		not specified	Likely benign (Apr 25, 2023)
2-46758588-G-C		not specified	Uncertain significance (Nov 17, 2022)
2-46758624-A-G		not specified	Uncertain significance (May 09, 2023)
2-46758656-G-C		not specified	Uncertain significance (Nov 10, 2022)
2-46758681-A-G		not specified	Likely benign (Aug 12, 2021)
2-46758695-A-C		not specified	Uncertain significance (Jun 10, 2024)
2-46758702-C-A		not specified	Uncertain significance (Nov 12, 2021)
2-46758712-A-C		not specified	Uncertain significance (May 31, 2023)
2-46758774-T-G		not specified	Uncertain significance (Oct 06, 2022)
2-46758813-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-46758843-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-46758877-G-T		not specified	Uncertain significance (May 17, 2024)
2-46758931-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-46758945-G-C		not specified	Uncertain significance (Dec 16, 2022)
2-46758963-A-G		not specified	Uncertain significance (Jul 13, 2022)
2-46759002-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-46759002-G-C		not specified	Uncertain significance (Nov 17, 2022)
2-46759029-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-46759032-T-G		not specified	Uncertain significance (Nov 14, 2023)
2-46759057-C-G		not specified	Uncertain significance (Jul 25, 2023)
2-46759063-G-C		not specified	Uncertain significance (Jul 06, 2021)
2-46759114-G-A		not specified	Likely benign (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC01118	protein_coding	protein_coding	ENST00000409912	4	5990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.91e-9	0.0193	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.131	68	65.0	1.05	0.00000314	826
Missense in Polyphen		5	4.3464	1.1504		49
Synonymous	0.285	22	23.8	0.926	0.00000127	222
Loss of Function	-1.43	11	6.93	1.59	2.97e-7	75

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: 0.394

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium