LIMA1

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

Basic information

Region (hg38): 12:50175787-50283520

Links

ENSG00000050405 ∙ NCBI:51474 ∙ OMIM:608364 ∙ HGNC:24636 ∙ Uniprot:Q9UHB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Low density lipoprotein cholesterol level quantitative trait locus	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal	29880681

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIMA1 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMA1 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	24	1	0

Variants in LIMA1

This is a list of pathogenic ClinVar variants found in the LIMA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50177123-A-C		not specified	Uncertain significance (Jun 28, 2023)
12-50177221-G-A		not specified	Uncertain significance (Jan 10, 2023)
12-50177245-T-C		not specified	Uncertain significance (Dec 28, 2022)
12-50177257-T-G		not specified	Uncertain significance (Dec 28, 2022)
12-50177296-C-T		not specified	Uncertain significance (Mar 28, 2023)
12-50177346-A-C		not specified	Uncertain significance (May 24, 2023)
12-50177373-T-G		not specified	Uncertain significance (Jan 03, 2024)
12-50177495-T-C		not specified	Uncertain significance (Dec 15, 2023)
12-50177536-T-G		not specified	Uncertain significance (Mar 22, 2023)
12-50177648-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-50177740-G-T		not specified	Uncertain significance (Oct 24, 2023)
12-50177753-C-T		not specified	Uncertain significance (Jul 06, 2022)
12-50177822-T-A		not specified	Uncertain significance (Aug 13, 2021)
12-50177852-T-C		not specified	Uncertain significance (Jul 12, 2023)
12-50177908-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-50177933-T-C		not specified	Uncertain significance (May 23, 2023)
12-50178049-A-G		not specified	Uncertain significance (Feb 10, 2022)
12-50192492-G-A		not specified	Uncertain significance (Dec 06, 2022)
12-50192510-A-C		not specified	Uncertain significance (Jan 23, 2023)
12-50195891-C-A		LIMA1-related disorder	Likely benign (Jun 03, 2019)
12-50195891-CAAAA-C		LIMA1-related disorder	Likely benign (Aug 28, 2019)
12-50200825-ATTCTCCTT-A		LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8	association (Aug 08, 2018)
12-50204673-G-A		not specified	Likely benign (Dec 04, 2023)
12-50206013-T-C		not specified	Uncertain significance (Feb 27, 2024)
12-50206062-G-A		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIMA1	protein_coding	protein_coding	ENST00000394943	10	107759

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.75e-10	0.974	125662	0	85	125747	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	316	401	0.788	0.0000201	5035
Missense in Polyphen		59	94.758	0.62264		1173
Synonymous	-0.297	150	145	1.03	0.00000758	1414
Loss of Function	2.24	21	35.4	0.594	0.00000199	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000987	0.000984
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000164	0.000163
Finnish	0.000191	0.000185
European (Non-Finnish)	0.000362	0.000360
Middle Eastern	0.000164	0.000163
South Asian	0.000296	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin-binding protein involved in actin cytoskeleton regulation and dynamics. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments (PubMed:12566430). Plays a role in cholesterol homeostasis. Influences plasma cholesterol levels through regulation of intestinal cholesterol absorption. May act as a scaffold protein by regulating NPC1L1 transportation, an essential protein for cholesterol absorption, to the plasma membrane by recruiting MYO5B to NPC1L1, and thus facilitates cholesterol uptake (By similarity). {ECO:0000250|UniProtKB:Q9ERG0, ECO:0000269|PubMed:12566430}.
• Pathway: Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.137
• rvis_EVS: -1
• rvis_percentile_EVS: 8.37

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.489
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lima1
• Phenotype: liver/biliary system phenotype; 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); digestive/alimentary phenotype; skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cholesterol metabolic process;cell migration;intestinal cholesterol absorption;negative regulation of actin filament depolymerization;ruffle organization;cholesterol homeostasis;actin filament bundle assembly
• Cellular component: stress fiber;ruffle;cytosol;plasma membrane;focal adhesion;actin cytoskeleton;brush border membrane;cleavage furrow
• Molecular function: actin monomer binding;protein binding;cadherin binding;metal ion binding;actin filament binding