LSMEM1

leucine rich single-pass membrane protein 1

Basic information

Region (hg38): 7:112480853-112491062

Previous symbols: [ "C7orf53" ]

Links

ENSG00000181016 ∙ NCBI:286006 ∙ ∙ HGNC:22036 ∙ Uniprot:Q8N8F7 ∙ 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 LSMEM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSMEM1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in LSMEM1

This is a list of pathogenic ClinVar variants found in the LSMEM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-112484925-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-112487017-C-A		not specified	Uncertain significance (Jun 06, 2023)
7-112489813-A-G		not specified	Uncertain significance (Jan 03, 2022)
7-112489870-T-C		not specified	Uncertain significance (Dec 13, 2023)
7-112489909-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-112489933-A-G		not specified	Uncertain significance (Mar 26, 2024)
7-112489939-A-T		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSMEM1	protein_coding	protein_coding	ENST00000312849	3	10210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000362	0.399	125719	0	26	125745	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.204	75	70.2	1.07	0.00000363	852
Missense in Polyphen		19	18.274	1.0397		240
Synonymous	0.164	27	28.1	0.961	0.00000151	265
Loss of Function	-0.0535	5	4.87	1.03	3.00e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000334
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.170
• ghis: 0.512

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: Lsmem1

Gene ontology

• Cellular component: cytosol;integral component of membrane
• Molecular function: protein binding