LIMD2

LIM domain containing 2, the group of LIM domain containing

Basic information

Region (hg38): 17:63695888-63701172

Links

ENSG00000136490 ∙ NCBI:80774 ∙ ∙ HGNC:28142 ∙ Uniprot:Q9BT23 ∙ 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 LIMD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMD2 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 LIMD2

This is a list of pathogenic ClinVar variants found in the LIMD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63698577-A-G		not specified	Uncertain significance (Jul 20, 2021)
17-63698665-G-A		not specified	Uncertain significance (Mar 09, 2025)
17-63698844-A-G		not specified	Uncertain significance (Feb 17, 2024)
17-63698853-T-C		not specified	Uncertain significance (Aug 20, 2024)
17-63698922-G-T		not specified	Uncertain significance (Dec 01, 2022)
17-63698937-G-A		not specified	Uncertain significance (Dec 03, 2024)
17-63699051-T-C		not specified	Uncertain significance (May 22, 2023)
17-63699258-T-C		not specified	Uncertain significance (Nov 07, 2022)
17-63699277-C-T		not specified	Uncertain significance (Jul 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIMD2	protein_coding	protein_coding	ENST00000259006	4	5271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.779	125553	0	4	125557	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.615	62	77.2	0.803	0.00000436	824
Missense in Polyphen		13	28.046	0.46353		328
Synonymous	0.651	29	33.8	0.858	0.00000220	227
Loss of Function	1.56	2	6.20	0.322	2.63e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an activator of the protein-kinase ILK, thereby regulating cell motility (PubMed:24590809). {ECO:0000269|PubMed:24590809}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.437
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.374
• hipred: Y
• hipred_score: 0.579
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Limd2

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding;metal ion binding