LYRM2

LYR motif containing 2, the group of LYR motif containing

Basic information

Region (hg38): 6:89568144-89638749

Links

ENSG00000083099 ∙ NCBI:57226 ∙ ∙ HGNC:25229 ∙ Uniprot:Q9NU23 ∙ 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 LYRM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYRM2 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			47	7	11	65
Total	0	0	48	7	11

Variants in LYRM2

This is a list of pathogenic ClinVar variants found in the LYRM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89595923-G-A		not specified	Uncertain significance (Mar 30, 2024)
6-89603051-G-A		not specified	Uncertain significance (Nov 03, 2022)
6-89603051-G-T		not specified	Uncertain significance (Jan 10, 2022)
6-89603087-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-89606052-C-G		ANKRD6-related disorder	Benign (Feb 19, 2020)
6-89606057-A-G			Benign (May 21, 2018)
6-89606069-C-T		ANKRD6-related disorder	Likely benign (Sep 17, 2019)
6-89606070-A-G		ANKRD6-related disorder	Benign (Oct 17, 2019)
6-89606091-C-G		not specified	Uncertain significance (Aug 08, 2023)
6-89612273-C-T		not specified	Uncertain significance (Mar 21, 2024)
6-89612308-A-C		not specified	Uncertain significance (Apr 13, 2022)
6-89612311-C-T		not specified	Uncertain significance (Dec 27, 2023)
6-89612325-G-A		ANKRD6-related disorder	Likely benign (Apr 09, 2019)
6-89612326-C-T		not specified	Uncertain significance (Jan 31, 2023)
6-89612329-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-89612350-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-89612351-G-A		not specified	Uncertain significance (Oct 24, 2023)
6-89613802-C-A		not specified	Uncertain significance (Aug 02, 2021)
6-89613813-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-89613820-C-T		not specified	Uncertain significance (Nov 09, 2023)
6-89613821-G-A			Likely benign (Jul 01, 2022)
6-89613822-C-T		not specified	Uncertain significance (Mar 23, 2022)
6-89613835-T-G		not specified	Uncertain significance (Jan 04, 2022)
6-89613840-A-G		not specified	Uncertain significance (May 31, 2023)
6-89613849-C-T		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYRM2	protein_coding	protein_coding	ENST00000523377	3	70610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000258	0.339	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.470	57	47.9	1.19	0.00000267	564
Missense in Polyphen		15	13.282	1.1294		191
Synonymous	0.134	16	16.7	0.958	8.10e-7	169
Loss of Function	-0.267	5	4.40	1.14	1.86e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000260	0.000260
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000985	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.497
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.240
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyrm2

Gene ontology

• Molecular function: protein binding