LYRM9

LYR motif containing 9, the group of LYR motif containing

Basic information

Region (hg38): 17:27878313-27894752

Previous symbols: [ "C17orf108" ]

Links

ENSG00000232859 ∙ NCBI:201229 ∙ ∙ HGNC:27314 ∙ Uniprot:A8MSI8 ∙ 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 LYRM9 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYRM9 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in LYRM9

This is a list of pathogenic ClinVar variants found in the LYRM9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-27880319-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-27882612-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-27882630-C-T		not specified	Uncertain significance (Oct 13, 2023)
17-27882631-G-A		not specified	Uncertain significance (Aug 16, 2022)
17-27882676-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYRM9	protein_coding	protein_coding	ENST00000379103	3	16439

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0147	0.700	119600	0	18	119618	0.0000752

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	33	38.9	0.849	0.00000215	494
Missense in Polyphen		22	21.772	1.0105		285
Synonymous	-0.169	15	14.2	1.06	7.42e-7	137
Loss of Function	0.634	3	4.44	0.675	2.65e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000284
Ashkenazi Jewish	0.000104	0.000102
East Asian	0.000121	0.000114
Finnish	0.00	0.00
European (Non-Finnish)	0.00000968	0.00000923
Middle Eastern	0.000121	0.000114
South Asian	0.000220	0.000208
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyrm9
• Phenotype: skeleton phenotype