LYSMD1

LysM domain containing 1

Basic information

Region (hg38): 1:151159747-151165948

Links

ENSG00000163155 ∙ NCBI:388695 ∙ ∙ HGNC:32070 ∙ Uniprot:Q96S90 ∙ 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 LYSMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYSMD1 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 LYSMD1

This is a list of pathogenic ClinVar variants found in the LYSMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151160913-C-T		not specified	Uncertain significance (May 01, 2024)
1-151160928-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-151161872-C-G		not specified	Uncertain significance (Jan 26, 2022)
1-151161928-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-151161944-T-A		not specified	Uncertain significance (Jun 16, 2023)
1-151161983-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-151162037-G-C		not specified	Uncertain significance (May 23, 2023)
1-151165092-T-C		not specified	Uncertain significance (Apr 28, 2023)
1-151165177-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-151165185-C-T		not specified	Uncertain significance (Jan 10, 2023)
1-151165245-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-151165248-G-A		not specified	Uncertain significance (Mar 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYSMD1	protein_coding	protein_coding	ENST00000368908	3	6201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.901	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.731	109	133	0.821	0.00000746	1444
Missense in Polyphen		39	50.896	0.76627		542
Synonymous	0.463	47	51.2	0.918	0.00000243	493
Loss of Function	1.48	4	8.69	0.460	4.66e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000574	0.000574
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.473
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0967
• hipred: N
• hipred_score: 0.200
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lysmd1

Gene ontology

• Cellular component: nucleus;nucleoplasm
• Molecular function: protein binding