LINC01556

long intergenic non-protein coding RNA 1556, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 6:28922706-28944717

Previous symbols: [ "C6orf100" ]

Links

ENSG00000204709 ∙ NCBI:729583 ∙ ∙ HGNC:21195 ∙ Uniprot:Q5JQF7 ∙ 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 LINC01556 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC01556 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 LINC01556

This is a list of pathogenic ClinVar variants found in the LINC01556 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28923275-G-C		not specified	Uncertain significance (Oct 10, 2023)
6-28923329-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-28923386-T-A		not specified	Uncertain significance (Dec 13, 2021)
6-28923479-A-G		not specified	Uncertain significance (Apr 22, 2022)
6-28923571-T-C		not specified	Uncertain significance (May 24, 2023)
6-28923598-T-C		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC01556	protein_coding	protein_coding	ENST00000377186	2	661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.396	0.482	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.542	15	22.2	0.676	9.78e-7	388
Missense in Polyphen		7	6.1996	1.1291		104
Synonymous	0.748	6	8.83	0.680	3.99e-7	120
Loss of Function	0.939	0	1.03	0.00	4.50e-8	17

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

• pHI: 0.0677