LSAMP

limbic system associated membrane protein, the group of I-set domain containing|IgLON cell adhesion molecules

Basic information

Region (hg38): 3:115802362-117139389

Links

ENSG00000185565 ∙ NCBI:4045 ∙ OMIM:603241 ∙ HGNC:6705 ∙ Uniprot:Q13449 ∙ 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 LSAMP gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSAMP 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in LSAMP

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

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

Position	Type	Phenotype	Significance	ClinVar
3-115810402-A-G		not specified	Uncertain significance (Aug 17, 2022)
3-115841985-C-T		not specified	Uncertain significance (Dec 26, 2023)
3-115852512-T-A		not specified	Uncertain significance (Jan 05, 2022)
3-116019517-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-116019562-T-C		not specified	Uncertain significance (Jan 04, 2022)
3-116019618-G-C		not specified	Uncertain significance (Sep 17, 2021)
3-116086417-G-C		not specified	Uncertain significance (Jun 01, 2023)
3-116086428-C-T		not specified	Uncertain significance (May 18, 2022)
3-116086536-T-C		not specified	Uncertain significance (Mar 02, 2023)
3-116445010-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSAMP	protein_coding	protein_coding	ENST00000490035	7	2194861

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0126	124245	0	1	124246	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	132	193	0.682	0.0000105	2165
Missense in Polyphen		33	75.305	0.43822		864
Synonymous	0.393	75	79.5	0.944	0.00000461	708
Loss of Function	3.67	1	17.6	0.0567	9.39e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000551
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000551	0.0000551
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates selective neuronal growth and axon targeting. Contributes to the guidance of developing axons and remodeling of mature circuits in the limbic system. Essential for normal growth of the hyppocampal mossy fiber projection (By similarity). {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.413
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.721
• hipred: Y
• hipred_score: 0.774
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsamp
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;nervous system development;locomotory exploration behavior
• Cellular component: extracellular region;cytosol;plasma membrane;anchored component of membrane
• Molecular function: protein binding