TH2LCRR

T helper type 2 locus control region associated RNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 5:132629735-132664272

Links

ENSG00000223442 ∙ NCBI:101927761 ∙ ∙ HGNC:40495 ∙ ∙ ∙ 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 TH2LCRR gene.

• Hereditary cancer-predisposing syndrome (598 variants)
• Nijmegen breakage syndrome-like disorder (56 variants)
• not provided (26 variants)
• not specified (16 variants)
• Familial cancer of breast (5 variants)
• Inborn genetic diseases (5 variants)
• Ovarian cancer (5 variants)
• RAD50-related condition (3 variants)
• Hereditary breast ovarian cancer syndrome (3 variants)
• Inherited susceptibility to asthma (2 variants)
• Premature ovarian insufficiency (1 variants)
• Allergic rhinitis, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TH2LCRR 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)	1	7	32	10		50
splice region						0
non coding	17	26	327	192	12	574
Total	18	33	359	202	12

Highest pathogenic variant AF is 0.0000329

Variants in TH2LCRR

This is a list of pathogenic ClinVar variants found in the TH2LCRR region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132637095-C-G		Hereditary cancer-predisposing syndrome	Likely benign (Feb 28, 2021)
5-132637095-C-T		Hereditary cancer-predisposing syndrome	Likely benign (Aug 30, 2023)
5-132637098-A-G		Hereditary cancer-predisposing syndrome	Likely benign (Mar 16, 2023)
5-132637105-C-T		Hereditary cancer-predisposing syndrome • not specified	Conflicting classifications of pathogenicity (Sep 29, 2022)
5-132637106-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Feb 18, 2022)
5-132637106-C-T		Hereditary cancer-predisposing syndrome	Likely benign (Oct 28, 2023)
5-132637110-T-A		Hereditary cancer-predisposing syndrome	Uncertain significance (Mar 13, 2023)
5-132637110-T-C		not specified • Hereditary cancer-predisposing syndrome	Conflicting classifications of pathogenicity (Nov 20, 2023)
5-132637110-T-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Jun 27, 2023)
5-132637111-C-T		Hereditary cancer-predisposing syndrome	Likely benign (Nov 01, 2018)
5-132637112-C-T		Hereditary cancer-predisposing syndrome	Uncertain significance (Nov 15, 2018)
5-132637113-A-G		Hereditary cancer-predisposing syndrome	Likely pathogenic (Oct 17, 2022)
5-132637114-G-A		Hereditary cancer-predisposing syndrome	Likely pathogenic (Jun 14, 2024)
5-132637115-A-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Jul 23, 2020)
5-132637116-G-A		Hereditary cancer-predisposing syndrome	Uncertain significance (Nov 28, 2020)
5-132637117-C-A		Hereditary cancer-predisposing syndrome	Uncertain significance (Jul 13, 2022)
5-132637117-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Feb 24, 2020)
5-132637119-A-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Jan 27, 2022)
5-132637122-A-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Sep 17, 2019)
5-132637125-A-C		Hereditary cancer-predisposing syndrome	Uncertain significance (Jul 24, 2022)
5-132637127-A-G		Hereditary cancer-predisposing syndrome	Likely benign (Jan 29, 2024)
5-132637130-T-C		Hereditary cancer-predisposing syndrome	Likely benign (Apr 08, 2023)
5-132637133-C-G		Hereditary cancer-predisposing syndrome	Uncertain significance (Jul 23, 2023)
5-132637133-C-T		Hereditary cancer-predisposing syndrome	Likely benign (Nov 29, 2022)
5-132637134-A-C		Hereditary cancer-predisposing syndrome	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP