LASP1

LIM and SH3 protein 1, the group of MicroRNA protein coding host genes|LIM domain containing

Basic information

Region (hg38): 17:38869858-38921770

Links

ENSG00000002834

∙ NCBI:3927 ∙ OMIM:602920 ∙ HGNC:6513 ∙ Uniprot:Q14847 ∙ 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 LASP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LASP1 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				1 clinvar	2 clinvar	3
missense			10 clinvar			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	1	2

Variants in LASP1

This is a list of pathogenic ClinVar variants found in the LASP1 region.

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

Position	Phenotype	Significance	ClinVar
17-38878112-C-T		Benign (Jul 10, 2018)	728929
17-38890461-C-T	Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)	981819
17-38898467-C-T	not specified	Uncertain significance (Mar 27, 2023)	2529941
17-38898478-G-A	not specified	Uncertain significance (Sep 28, 2022)	2311113
17-38914358-A-G	not specified	Uncertain significance (Feb 13, 2024)	3117926
17-38914401-A-T	not specified	Uncertain significance (Jul 19, 2022)	2215338
17-38914461-C-T	not specified	Uncertain significance (Feb 28, 2023)	2473157
17-38914462-G-A		Likely benign (May 31, 2018)	745719
17-38915118-T-C	not specified	Uncertain significance (Oct 04, 2022)	2366872
17-38915129-G-A	not specified	Uncertain significance (Aug 02, 2022)	2304744
17-38915138-G-C	not specified	Uncertain significance (Sep 30, 2022)	2388366
17-38915144-G-A	not specified	Uncertain significance (Jun 18, 2024)	3290168
17-38918616-C-T		Benign (Mar 06, 2018)	778689
17-38918701-G-A	not specified	Uncertain significance (Nov 09, 2022)	2324886

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LASP1	protein_coding	protein_coding	ENST00000318008	7	51912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0173	125725	0	2	125727	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	101	186	0.544	0.0000128	1732
Missense in Polyphen		24	67.327	0.35647		568
Synonymous	0.223	74	76.5	0.968	0.00000608	444
Loss of Function	3.57	1	16.8	0.0597	8.14e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.000272	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays an important role in the regulation of dynamic actin-based, cytoskeletal activities. Agonist-dependent changes in LASP1 phosphorylation may also serve to regulate actin-associated ion transport activities, not only in the parietal cell but also in certain other F-actin-rich secretory epithelial cell types (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

loftool: 0.408
rvis_EVS: -0.45
rvis_percentile_EVS: 24

Haploinsufficiency Scores

pHI: 0.333
hipred: Y
hipred_score: 0.662
ghis: 0.631

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lasp1
Phenotype: skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: ion transport;positive regulation of signal transduction;ion transmembrane transport
Cellular component: cytoplasm;focal adhesion;cortical actin cytoskeleton
Molecular function: SH3/SH2 adaptor activity;protein binding;ion transmembrane transporter activity;cadherin binding;metal ion binding;actin filament binding