CHROMR

cholesterol induced regulator of metabolism RNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 2:178413476-178442854

Previous symbols: [ "PRKRA-AS1" ]

Links

ENSG00000223960 ∙ NCBI:101927027 ∙ ∙ HGNC:54059 ∙ ∙ ∙ 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 CHROMR gene.

• Dystonia 16 (49 variants)
• not provided (18 variants)
• Dystonic disorder (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHROMR 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			1
splice region						0
non coding	1	2	23	21	7	54
Total	1	2	24	21	7

Highest pathogenic variant AF is 0.000974

Variants in CHROMR

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

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

Position	Type	Phenotype	Significance	ClinVar
2-178431442-A-G		Dystonia 16	Uncertain significance (Jan 13, 2018)
2-178431521-C-T		Dystonia 16	Uncertain significance (Jan 13, 2018)
2-178431521-C-CACA		Dystonic disorder	Benign (Jun 14, 2016)
2-178431544-T-C		Dystonia 16	Uncertain significance (Jan 12, 2018)
2-178431654-ACAAT-A		Dystonic disorder	Benign (Jun 14, 2016)
2-178431784-C-T		Dystonia 16	Conflicting classifications of pathogenicity (Jul 09, 2018)
2-178431832-T-G		Dystonia 16	Uncertain significance (Jan 13, 2018)
2-178431897-C-T		Dystonia 16	Benign/Likely benign (Jul 09, 2018)
2-178431899-G-A		Dystonia 16	Benign (Jul 09, 2018)
2-178431917-G-A		Dystonia 16	Uncertain significance (Jan 13, 2018)
2-178431938-A-G		Dystonia 16	Benign/Likely benign (Feb 04, 2019)
2-178431939-T-C		Dystonia 16	Conflicting classifications of pathogenicity (Jul 09, 2018)
2-178431946-T-A		Dystonia 16	Uncertain significance (Jan 12, 2018)
2-178432018-C-T		Dystonia 16	Uncertain significance (Jan 13, 2018)
2-178432066-C-T		Dystonia 16	Likely benign (Jan 13, 2018)
2-178432094-G-A		Dystonia 16	Benign (Aug 03, 2018)
2-178432116-A-G		Dystonia 16	Uncertain significance (Jul 23, 2020)
2-178432137-T-C		Dystonia 16	Uncertain significance (Dec 29, 2020)
2-178432148-A-G		Dystonia 16	Likely benign (Mar 02, 2020)
2-178432169-G-A		Dystonia 16	Uncertain significance (Jan 12, 2018)
2-178432178-G-A		Dystonia 16	Likely benign (Jul 14, 2022)
2-178432178-G-T		Dystonia 16	Uncertain significance (Sep 11, 2023)
2-178432179-G-C		Inborn genetic diseases	Uncertain significance (May 14, 2024)
2-178432185-T-C		Dystonia 16	Uncertain significance (May 25, 2022)
2-178432188-C-A		Dystonia 16	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP