LINC02908

long intergenic non-protein coding RNA 2908, the group of Long intergenic non-protein coding RNAs

Basic information

Region (hg38): 9:137027464-137037957

Previous symbols: [ "C9orf139" ]

Links

ENSG00000180539 ∙ NCBI:401563 ∙ ∙ HGNC:31426 ∙ Uniprot:Q6ZV77 ∙ 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 LINC02908 gene.

• Inborn genetic diseases (27 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINC02908 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			27	2	4	33
Total	0	0	27	2	4

Variants in LINC02908

This is a list of pathogenic ClinVar variants found in the LINC02908 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137028099-G-C		Intellectual developmental disorder with poor growth and with or without seizures or ataxia	Uncertain significance (Mar 25, 2024)
9-137028748-C-T		not specified	Uncertain significance (Oct 22, 2021)
9-137028776-AG-A			Uncertain significance (Nov 01, 2019)
9-137028794-C-G		not specified	Uncertain significance (Aug 09, 2021)
9-137028813-A-G			Benign (Oct 23, 2019)
9-137028867-C-T			Likely benign (Apr 01, 2022)
9-137028872-T-C		ABCA2-related disorder	Benign (Jul 13, 2018)
9-137030727-C-T		not specified	Uncertain significance (Apr 08, 2024)
9-137030768-T-A		not specified	Uncertain significance (May 31, 2023)
9-137030769-A-G			Benign (May 15, 2018)
9-137030781-T-G		not specified	Uncertain significance (Mar 29, 2022)
9-137030799-G-A		not specified	Uncertain significance (Nov 08, 2022)
9-137030805-C-T		not specified	Uncertain significance (Mar 19, 2024)
9-137030820-C-T		not specified	Uncertain significance (Apr 09, 2024)
9-137030834-C-T		not specified	Uncertain significance (Mar 19, 2024)
9-137030846-A-C		not specified	Uncertain significance (May 03, 2023)
9-137030858-C-T		not specified	Uncertain significance (Apr 25, 2022)
9-137030892-G-C		not specified	Uncertain significance (Jun 16, 2023)
9-137030912-T-C		not specified	Uncertain significance (Jun 17, 2022)
9-137030990-G-A		not specified	Uncertain significance (May 23, 2023)
9-137030994-C-T			Benign (Jun 29, 2018)
9-137031011-C-G		not specified	Uncertain significance (Dec 19, 2022)
9-137031026-G-A		not specified	Uncertain significance (May 18, 2023)
9-137031071-C-T		not specified	Uncertain significance (Mar 29, 2022)
9-137031105-C-T		not specified	Likely benign (Nov 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINC02908	protein_coding	protein_coding	ENST00000314330	2	9319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00246	0.344	124901	0	10	124911	0.0000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.277	127	119	1.07	0.00000674	1193
Missense in Polyphen		9	10.466	0.85994		89
Synonymous	-0.833	59	51.4	1.15	0.00000298	438
Loss of Function	-1.06	3	1.57	1.91	6.68e-8	17

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000178
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000335	0.000328

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.757
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.0742
• hipred: N
• hipred_score: 0.146
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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