LINC01551

long intergenic non-protein coding RNA 1551, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 14:28765640-28823817

Previous symbols: [ "C14orf23" ]

Links

ENSG00000186960 ∙ NCBI:387978 ∙ ∙ HGNC:19828 ∙ Uniprot:Q86U37 ∙ AlphaFold ∙ 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 LINC01551 gene.

• Rett syndrome, congenital variant (526 variants)
• not provided (226 variants)
• Inborn genetic diseases (92 variants)
• not specified (76 variants)
• FOXG1 disorder (40 variants)
• FOXG1-related condition (9 variants)
• Neurodevelopmental disorder (2 variants)
• Intellectual disability (2 variants)
• Intellectual disability, severe;Primary microcephaly;Aplasia/Hypoplasia of the corpus callosum (1 variants)
• Abnormal cerebral morphology (1 variants)
• Neurodevelopmental abnormality (1 variants)
• See cases (1 variants)
• Autism spectrum disorder (1 variants)
• Strabismus;Abnormal optic nerve morphology;Axial hypotonia;Stereotypic movement disorder;Global developmental delay (1 variants)
• Abnormality of the nervous system (1 variants)
• Lissencephaly (1 variants)
• Rett syndrome (1 variants)
• Severe intellectual deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01551 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	155	75	154	271	36	691
Total	155	75	154	271	36

Variants in LINC01551

This is a list of pathogenic ClinVar variants found in the LINC01551 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-28766942-C-CA			Benign (Nov 19, 2019)
14-28766942-C-CG			Likely benign (Nov 14, 2019)
14-28767011-G-C			Likely benign (Jun 19, 2018)
14-28767055-CT-C			Likely benign (Aug 21, 2019)
14-28767055-C-CT			Likely benign (Aug 15, 2019)
14-28767254-C-G		not specified	Likely benign (Jun 17, 2016)
14-28767262-C-T		not specified	Likely benign (Sep 23, 2016)
14-28767280-A-T		Rett syndrome, congenital variant	Uncertain significance (Aug 30, 2023)
14-28767284-T-TGAACGA		Rett syndrome, congenital variant	Uncertain significance (Sep 22, 2024)
14-28767288-C-T		not specified	Likely benign (Jan 13, 2017)
14-28767289-A-G			Uncertain significance (Dec 03, 2023)
14-28767300-G-A		Rett syndrome, congenital variant	Uncertain significance (Jan 10, 2024)
14-28767301-AAAG-A		Rett syndrome, congenital variant	Uncertain significance (Oct 05, 2023)
14-28767306-G-A		Rett syndrome, congenital variant	Uncertain significance (Dec 17, 2023)
14-28767318-C-T		Rett syndrome, congenital variant	Likely benign (Jan 24, 2020)
14-28767319-C-T		Rett syndrome, congenital variant	Uncertain significance (Feb 08, 2022)
14-28767325-T-C		Rett syndrome, congenital variant	Uncertain significance (May 20, 2023)
14-28767336-C-T		not specified • Rett syndrome, congenital variant	Likely benign (Jul 12, 2022)
14-28767357-G-A		Rett syndrome, congenital variant	Likely benign (Feb 03, 2022)
14-28767360-G-A		Rett syndrome, congenital variant	Likely benign (Oct 29, 2021)
14-28767362-TC-T		Rett syndrome, congenital variant	Pathogenic (May 28, 2019)
14-28767364-C-T			Pathogenic (Sep 01, 2022)
14-28767369-C-T		Rett syndrome, congenital variant	Likely benign (Sep 27, 2022)
14-28767370-G-A			Likely benign (Apr 05, 2021)
14-28767374-A-G		Rett syndrome, congenital variant • Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC01551	protein_coding	protein_coding	ENST00000399387	3	40584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.692	56	72.6	0.771	0.00000320	1075
Missense in Polyphen		3	3.1165	0.96263		40
Synonymous	1.04	21	28.0	0.750	0.00000132	320
Loss of Function	0.980	1	2.75	0.363	1.29e-7	29

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: 0.504

Essentials

• essential_gene_gene_trap: N