LYSMD4

LysM domain containing 4

Basic information

Region (hg38): 15:99715697-99733561

Links

ENSG00000183060 ∙ NCBI:145748 ∙ ∙ HGNC:26571 ∙ Uniprot:Q5XG99 ∙ 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 LYSMD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYSMD4 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in LYSMD4

This is a list of pathogenic ClinVar variants found in the LYSMD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-99729148-C-T		not specified	Uncertain significance (Sep 03, 2024)
15-99729172-A-T		not specified	Uncertain significance (May 26, 2023)
15-99729184-G-C		not specified	Uncertain significance (Nov 21, 2023)
15-99729190-G-C		not specified	Uncertain significance (Oct 23, 2024)
15-99729237-A-T		not specified	Uncertain significance (Nov 14, 2024)
15-99729238-T-A		not specified	Uncertain significance (Jan 08, 2024)
15-99729238-T-C		not specified	Uncertain significance (Oct 31, 2024)
15-99729380-C-T		not specified	Uncertain significance (Nov 17, 2023)
15-99729449-C-G		not specified	Uncertain significance (Jun 23, 2021)
15-99729461-T-C		not specified	Uncertain significance (Aug 04, 2023)
15-99729529-T-G		not specified	Uncertain significance (Sep 22, 2021)
15-99729539-T-G		not specified	Uncertain significance (Jul 14, 2021)
15-99729545-C-T		not specified	Likely benign (Aug 03, 2022)
15-99729566-G-C		not specified	Uncertain significance (Oct 01, 2024)
15-99729575-C-T		not specified	Uncertain significance (Nov 21, 2024)
15-99729590-C-T		not specified	Uncertain significance (Nov 07, 2022)
15-99729661-A-C		not specified	Uncertain significance (Jun 06, 2023)
15-99729682-T-C		not specified	Uncertain significance (Aug 21, 2024)
15-99729683-A-G		not specified	Uncertain significance (Jun 26, 2024)
15-99731387-G-A		not specified	Uncertain significance (Aug 06, 2021)
15-99731737-G-A		not specified	Uncertain significance (Dec 08, 2024)
15-99731790-G-A		not specified	Uncertain significance (Jul 14, 2024)
15-99731802-C-G		not specified	Uncertain significance (Sep 04, 2024)
15-99731827-C-A		not specified	Uncertain significance (Jan 26, 2022)
15-99731836-C-T		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYSMD4	protein_coding	protein_coding	ENST00000344791	4	17865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000562	0.723	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00229	170	170	1.00	0.00000976	1947
Missense in Polyphen		31	33.991	0.912		492
Synonymous	0.0518	67	67.5	0.992	0.00000450	596
Loss of Function	0.891	6	8.86	0.677	3.79e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000114
Middle Eastern	0.00	0.00
South Asian	0.00115	0.00108
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 1.82
• rvis_percentile_EVS: 96.99

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.123
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lysmd4

Gene ontology

• Cellular component: integral component of membrane