LIMD1

LIM domain containing 1, the group of Ajuba family

Basic information

Region (hg38): 3:45555394-45686341

Links

ENSG00000144791 ∙ NCBI:8994 ∙ OMIM:604543 ∙ HGNC:6612 ∙ Uniprot:Q9UGP4 ∙ 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 LIMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMD1 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	1
missense			29	5		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	5	1

Variants in LIMD1

This is a list of pathogenic ClinVar variants found in the LIMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-45594902-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-45594937-A-G		not specified	Uncertain significance (Feb 14, 2023)
3-45594939-G-A		not specified	Uncertain significance (Jun 10, 2024)
3-45594976-A-C		not specified	Uncertain significance (Aug 04, 2023)
3-45595145-G-A		not specified	Likely benign (Dec 15, 2023)
3-45595162-A-T		not specified	Uncertain significance (Aug 04, 2023)
3-45595196-C-T		not specified	Uncertain significance (Mar 29, 2023)
3-45595219-C-T		not specified	Uncertain significance (Feb 07, 2023)
3-45595222-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-45595256-C-T		not specified	Likely benign (Jan 23, 2024)
3-45595337-G-A		not specified	Uncertain significance (Jun 06, 2023)
3-45595403-C-T		not specified	Uncertain significance (Feb 23, 2023)
3-45595450-G-A		not specified	Uncertain significance (Mar 31, 2023)
3-45595469-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-45595498-G-A		not specified	Uncertain significance (Mar 07, 2024)
3-45595514-C-G		not specified	Uncertain significance (Jun 07, 2024)
3-45595514-C-T		not specified	Likely benign (Mar 29, 2022)
3-45595546-G-A		not specified	Likely benign (Aug 02, 2021)
3-45595615-G-A		not specified	Uncertain significance (Nov 07, 2022)
3-45595622-A-G		not specified	Uncertain significance (Jan 16, 2024)
3-45595637-G-A		not specified	Uncertain significance (Jan 10, 2023)
3-45595688-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-45595783-G-A		not specified	Uncertain significance (May 16, 2023)
3-45595906-T-A		not specified	Uncertain significance (Jul 13, 2021)
3-45595937-C-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIMD1	protein_coding	protein_coding	ENST00000273317	8	130945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.417	0.583	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.477	368	395	0.932	0.0000214	4372
Missense in Polyphen		85	106.95	0.79478		1225
Synonymous	-0.407	173	166	1.04	0.00000981	1419
Loss of Function	3.76	6	27.1	0.221	0.00000149	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000209	0.000209
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000971	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG- dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1- responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation. {ECO:0000269|PubMed:15542589, ECO:0000269|PubMed:20303269, ECO:0000269|PubMed:20616046, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:22286099}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;Cellular responses to stress;Cellular responses to external stimuli;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.327
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.98

Haploinsufficiency Scores

• pHI: 0.395
• hipred: N
• hipred_score: 0.414
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Limd1
• Phenotype: immune system phenotype; hematopoietic system phenotype; skeleton phenotype

Gene ontology

• Biological process: response to hypoxia;osteoblast development;regulation of transcription, DNA-templated;cytoskeleton organization;signal transduction;multicellular organism development;regulation of cell shape;phosphorylation;cell migration;cytoplasmic mRNA processing body assembly;gene silencing by miRNA;negative regulation of hippo signaling;negative regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated;regulation of transcription from RNA polymerase II promoter in response to hypoxia;negative regulation of canonical Wnt signaling pathway;positive regulation of gene silencing by miRNA
• Cellular component: P-body;nucleus;transcription factor complex;cytoplasm;cytosol;plasma membrane;cell-cell junction;adherens junction;focal adhesion;RISC complex
• Molecular function: transcription corepressor activity;protein binding;zinc ion binding