LYSMD2

LysM domain containing 2

Basic information

Region (hg38): 15:51723011-51751585

Links

ENSG00000140280 ∙ NCBI:256586 ∙ ∙ HGNC:28571 ∙ Uniprot:Q8IV50 ∙ 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 LYSMD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYSMD2 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in LYSMD2

This is a list of pathogenic ClinVar variants found in the LYSMD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-51724892-G-A		not specified	Uncertain significance (Dec 27, 2022)
15-51724923-G-A		not specified	Uncertain significance (Aug 20, 2023)
15-51724953-C-T		not specified	Uncertain significance (Jan 18, 2023)
15-51724976-T-G		not specified	Uncertain significance (Oct 05, 2023)
15-51737400-C-T		not specified	Uncertain significance (Jan 23, 2024)
15-51737429-C-A		not specified	Uncertain significance (Nov 03, 2023)
15-51737430-C-T		not specified	Uncertain significance (Dec 13, 2023)
15-51737441-G-A		not specified	Uncertain significance (Nov 18, 2022)
15-51737469-A-G		not specified	Uncertain significance (Mar 01, 2024)
15-51737529-C-T		not specified	Uncertain significance (May 15, 2024)
15-51737543-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYSMD2	protein_coding	protein_coding	ENST00000267838	3	28575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.416	0.552	125701	0	6	125707	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.211	70	75.1	0.932	0.00000325	1358
Missense in Polyphen		18	26.222	0.68644		437
Synonymous	1.26	21	29.8	0.706	0.00000137	453
Loss of Function	1.71	1	5.20	0.192	2.18e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.240
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lysmd2