LSMEM2

leucine rich single-pass membrane protein 2

Basic information

Region (hg38): 3:50279087-50288114

Previous symbols: [ "C3orf45" ]

Links

ENSG00000179564 ∙ NCBI:132228 ∙ ∙ HGNC:26781 ∙ Uniprot:Q8N112 ∙ 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 LSMEM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSMEM2 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in LSMEM2

This is a list of pathogenic ClinVar variants found in the LSMEM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50279132-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-50286476-G-A		not specified	Likely benign (Sep 13, 2023)
3-50286485-A-G		not specified	Uncertain significance (Dec 13, 2022)
3-50286489-T-C		not specified	Likely benign (Apr 24, 2024)
3-50286559-G-C		not specified	Uncertain significance (Apr 24, 2024)
3-50286569-G-C		not specified	Uncertain significance (Dec 27, 2023)
3-50286718-G-A		not specified	Likely benign (Nov 08, 2022)
3-50286733-G-T		not specified	Uncertain significance (Nov 28, 2023)
3-50286743-C-T		not specified	Uncertain significance (Aug 14, 2023)
3-50286838-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-50286857-T-G		not specified	Uncertain significance (Mar 29, 2022)
3-50287105-C-T		not specified	Uncertain significance (Feb 23, 2023)
3-50287110-C-T		not specified	Uncertain significance (Apr 07, 2022)
3-50287140-C-T		not specified	Uncertain significance (Mar 13, 2023)
3-50287147-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSMEM2	protein_coding	protein_coding	ENST00000316436	4	9088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.36e-7	0.163	125492	1	243	125736	0.000971

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0391	104	105	0.989	0.00000676	1027
Missense in Polyphen		38	37.48	1.0139		413
Synonymous	0.578	45	50.2	0.896	0.00000335	368
Loss of Function	-0.216	9	8.33	1.08	5.52e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000787	0.000778
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00169	0.00169
Finnish	0.00380	0.00375
European (Non-Finnish)	0.000681	0.000677
Middle Eastern	0.00169	0.00169
South Asian	0.000951	0.000948
Other	0.000980	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.386
• hipred: N
• hipred_score: 0.123
• ghis: 0.530

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: Lsmem2

Gene ontology

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