LINC01664

long intergenic non-protein coding RNA 1664, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 22:17119519-17132113

Links

ENSG00000235478 ∙ NCBI:100996342 ∙ ∙ HGNC:52452 ∙ ∙ ∙ 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 LINC01664 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01664 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 LINC01664

This is a list of pathogenic ClinVar variants found in the LINC01664 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17119540-C-G		not specified	Uncertain significance (Jul 13, 2022)
22-17119564-C-T		not specified	Uncertain significance (Jan 08, 2024)
22-17119566-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-17119651-G-C		not specified	Uncertain significance (May 10, 2024)
22-17119699-C-T		not specified	Uncertain significance (Aug 10, 2021)
22-17119710-C-T		not specified	Uncertain significance (Feb 01, 2025)
22-17119719-C-T		not specified	Uncertain significance (Mar 01, 2025)
22-17119764-G-C		not specified	Uncertain significance (Nov 09, 2024)
22-17119787-G-C		not specified	Uncertain significance (Jan 17, 2025)
22-17119793-C-G		not specified	Uncertain significance (May 05, 2023)
22-17119837-C-A		not specified	Uncertain significance (Sep 01, 2024)
22-17119872-G-C		not specified	Uncertain significance (Dec 06, 2023)
22-17119894-G-C		not specified	Uncertain significance (Jun 22, 2023)
22-17119915-C-G		not specified	Uncertain significance (Dec 07, 2024)
22-17119935-C-T		not specified	Uncertain significance (Nov 17, 2022)
22-17119962-C-A		not specified	Uncertain significance (May 04, 2022)
22-17119963-G-A		not specified	Uncertain significance (Sep 04, 2024)
22-17119983-G-A		not specified	Uncertain significance (Sep 22, 2023)
22-17119984-G-A		not specified	Uncertain significance (Oct 26, 2022)
22-17119999-G-A		not specified	Uncertain significance (Aug 31, 2022)
22-17120005-C-T		not specified	Uncertain significance (May 23, 2023)
22-17120007-C-A		not specified	Uncertain significance (Jan 04, 2022)
22-17120008-C-T		not specified	Uncertain significance (Jan 14, 2025)
22-17120060-C-T		not specified	Uncertain significance (Jan 01, 2025)
22-17120098-G-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC01664	protein_coding	protein_coding	ENST00000441544	3	10519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.114	0.787	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	28	41.7	0.671	0.00000209	682
Missense in Polyphen		2	3.5436	0.56439		35
Synonymous	1.47	9	16.6	0.542	7.67e-7	197
Loss of Function	1.30	2	5.20	0.385	3.87e-7	66

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: 0.459