LYSMD3

LysM domain containing 3

Basic information

Region (hg38): 5:90515611-90529584

Links

ENSG00000176018 ∙ NCBI:116068 ∙ ∙ HGNC:26969 ∙ Uniprot:Q7Z3D4 ∙ 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 LYSMD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYSMD3 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				2		2
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in LYSMD3

This is a list of pathogenic ClinVar variants found in the LYSMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-90518893-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-90518914-T-A		not specified	Uncertain significance (May 08, 2023)
5-90518980-C-T		not specified	Uncertain significance (Nov 14, 2023)
5-90518989-G-T		not specified	Uncertain significance (Jun 12, 2023)
5-90519029-C-T			Likely benign (May 04, 2018)
5-90519095-T-C			Likely benign (Apr 20, 2018)
5-90519112-A-G		not specified	Uncertain significance (Jul 14, 2021)
5-90519156-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-90519157-G-A		not specified	Uncertain significance (May 16, 2022)
5-90519160-T-A			Benign (Dec 31, 2019)
5-90519180-G-A		not specified	Uncertain significance (May 16, 2023)
5-90519192-T-C		not specified	Uncertain significance (Sep 27, 2022)
5-90519289-G-A		not specified	Uncertain significance (Dec 20, 2021)
5-90519301-C-G		not specified	Uncertain significance (Mar 25, 2024)
5-90519348-C-T		not specified	Uncertain significance (Feb 10, 2022)
5-90519385-C-T		not specified	Uncertain significance (Aug 16, 2021)
5-90519390-A-G		not specified	Uncertain significance (May 27, 2022)
5-90519444-T-C		not specified	Uncertain significance (Mar 21, 2024)
5-90525058-T-C		not specified	Uncertain significance (Aug 17, 2022)
5-90525121-C-T		not specified	Uncertain significance (Nov 03, 2022)
5-90525168-T-A		not specified	Uncertain significance (May 24, 2024)
5-90525188-C-A		not specified	Uncertain significance (Jan 23, 2024)
5-90525201-C-T		not specified	Likely benign (Apr 05, 2023)
5-90525259-G-A		not specified	Uncertain significance (Dec 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYSMD3	protein_coding	protein_coding	ENST00000315948	2	13974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.304	0.693	124770	0	13	124783	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.324	151	163	0.928	0.00000825	2002
Missense in Polyphen		40	55.389	0.72216		694
Synonymous	0.805	47	54.6	0.861	0.00000270	575
Loss of Function	2.50	3	12.6	0.239	7.66e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000353
Middle Eastern	0.0000556	0.0000556
South Asian	0.000131	0.000131
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.764
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.261
• hipred: Y
• hipred_score: 0.530
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lysmd3

Gene ontology

• Cellular component: integral component of membrane