LIPT2-AS1

LIPT2 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 11:74493366-74498533

Links

ENSG00000254837 ∙ NCBI:100287896 ∙ ∙ HGNC:56172 ∙ ∙ ∙ 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 LIPT2-AS1 gene.

• not provided (49 variants)
• Inborn genetic diseases (10 variants)
• Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities (10 variants)
• Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPT2-AS1 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		3	40	16	3	62
Total	0	3	40	16	3

Highest pathogenic variant AF is 0.0000526

Variants in LIPT2-AS1

This is a list of pathogenic ClinVar variants found in the LIPT2-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74493373-G-A			Uncertain significance (Mar 27, 2022)
11-74493376-G-A			Likely benign (Jun 05, 2023)
11-74493378-C-G		not specified	Conflicting classifications of pathogenicity (Dec 17, 2023)
11-74493378-C-T		Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities • Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome	Uncertain significance (Mar 27, 2022)
11-74493383-A-C			Likely benign (Sep 19, 2022)
11-74493390-A-C		Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities	Pathogenic/Likely pathogenic (Oct 23, 2020)
11-74493391-G-C			Uncertain significance (Nov 29, 2022)
11-74493394-C-G		not specified	Uncertain significance (May 08, 2023)
11-74493396-A-C		not specified	Uncertain significance (Jan 04, 2024)
11-74493402-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-74493403-G-A		not specified	Uncertain significance (Sep 28, 2022)
11-74493416-C-G		Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities	Uncertain significance (Oct 13, 2021)
11-74493420-C-T		Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities	Uncertain significance (Sep 22, 2024)
11-74493422-C-G			Likely benign (Jan 10, 2024)
11-74493424-G-A			Uncertain significance (Aug 09, 2022)
11-74493427-C-T		not specified	Uncertain significance (Jul 09, 2021)
11-74493431-G-A		Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities	Benign/Likely benign (Jan 25, 2024)
11-74493434-G-T		LIPT2-related disorder	Benign (Dec 11, 2023)
11-74493441-A-C			Uncertain significance (Oct 24, 2022)
11-74493441-AGGCCACCGC-A			Uncertain significance (Jun 28, 2022)
11-74493451-G-A			Uncertain significance (Sep 05, 2021)
11-74493453-C-G			Uncertain significance (Dec 25, 2022)
11-74493463-G-A		not specified	Uncertain significance (Jan 11, 2023)
11-74493481-C-T			Uncertain significance (Nov 02, 2022)
11-74493491-C-T			Likely benign (Jul 06, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP