LYRM1

LYR motif containing 1, the group of LYR motif containing

Basic information

Region (hg38): 16:20899868-20925006

Links

ENSG00000102897 ∙ NCBI:57149 ∙ OMIM:614709 ∙ HGNC:25074 ∙ Uniprot:O43325 ∙ 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 LYRM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYRM1 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					1	1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	1

Variants in LYRM1

This is a list of pathogenic ClinVar variants found in the LYRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20915593-A-G		not specified	Uncertain significance (Mar 31, 2023)
16-20915595-C-T		not specified	Uncertain significance (Jul 14, 2021)
16-20915629-C-T		not specified	Uncertain significance (Nov 17, 2023)
16-20915676-C-T			Benign (Apr 04, 2018)
16-20920126-C-A		not specified	Uncertain significance (Nov 09, 2023)
16-20920167-G-A		not specified	Uncertain significance (Dec 15, 2021)
16-20920176-G-C		not specified	Uncertain significance (Feb 15, 2023)
16-20924009-C-T		not specified	Uncertain significance (Jan 06, 2023)
16-20924025-C-T		not specified	Uncertain significance (Dec 22, 2023)
16-20924049-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYRM1	protein_coding	protein_coding	ENST00000396052	3	25139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.72e-9	0.0285	125705	0	42	125747	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	80	70.2	1.14	0.00000405	781
Missense in Polyphen		24	22	1.0909		279
Synonymous	0.640	22	26.2	0.841	0.00000152	244
Loss of Function	-1.11	11	7.67	1.43	5.71e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May promote cell proliferation and inhibition of apoptosis of preadipocytes. {ECO:0000269|PubMed:19022914}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.299
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.350
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.488

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyrm1

Gene ontology

• Cellular component: nucleoplasm;midbody