LIMCH1

LIM and calponin homology domains 1, the group of LIM domain containing

Basic information

Region (hg38): 4:41359607-41700044

Links

ENSG00000064042 ∙ NCBI:22998 ∙ OMIM:617750 ∙ HGNC:29191 ∙ Uniprot:Q9UPQ0 ∙ 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 LIMCH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIMCH1 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				2		2
missense			70	4		74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	71	6	0

Variants in LIMCH1

This is a list of pathogenic ClinVar variants found in the LIMCH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-41360893-C-A		not specified	Uncertain significance (Feb 21, 2024)
4-41360899-C-G		not specified	Uncertain significance (Jun 21, 2022)
4-41494537-A-G		not specified	Uncertain significance (Mar 21, 2024)
4-41494552-G-A		not specified	Uncertain significance (Feb 28, 2024)
4-41494593-A-G		not specified	Uncertain significance (Jan 04, 2022)
4-41599004-A-G		not specified	Uncertain significance (Oct 20, 2021)
4-41603883-A-T		not specified	Uncertain significance (Feb 27, 2023)
4-41605954-A-G		not specified	Uncertain significance (May 23, 2023)
4-41605981-G-A		not specified	Uncertain significance (Feb 10, 2022)
4-41613613-T-G		not specified	Uncertain significance (Sep 27, 2021)
4-41613616-C-T		not specified	Uncertain significance (May 24, 2023)
4-41613622-A-C		not specified	Uncertain significance (Jul 20, 2021)
4-41619272-C-G		not specified	Uncertain significance (Mar 29, 2022)
4-41619389-G-T		not specified	Uncertain significance (Feb 16, 2023)
4-41619406-G-A		not specified	Uncertain significance (May 18, 2023)
4-41619415-C-G		not specified	Uncertain significance (Apr 09, 2024)
4-41632809-G-A			Likely benign (Feb 01, 2023)
4-41644510-A-G		not specified	Uncertain significance (Mar 01, 2023)
4-41644541-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-41646133-G-A		not specified	Uncertain significance (Jun 17, 2022)
4-41646490-G-A		not specified	Uncertain significance (Dec 12, 2023)
4-41646528-C-T		not specified	Uncertain significance (Feb 21, 2024)
4-41646537-G-C		not specified	Uncertain significance (Sep 29, 2023)
4-41646544-C-T		not specified	Uncertain significance (Oct 10, 2023)
4-41646582-A-G		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIMCH1	protein_coding	protein_coding	ENST00000313860	27	340438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.947	0.0527	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	564	600	0.940	0.0000338	7104
Missense in Polyphen		217	253.97	0.85444		2938
Synonymous	1.03	208	228	0.913	0.0000134	2034
Loss of Function	5.90	12	62.2	0.193	0.00000326	743

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00301	0.00301
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000984	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269|PubMed:28228547}.

Recessive Scores

• pRec: 0.0874

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.7

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.354
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0923

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Limch1

Gene ontology

• Biological process: positive regulation of protein phosphorylation;negative regulation of cell migration;actomyosin structure organization;positive regulation of stress fiber assembly;regulation of focal adhesion assembly
• Cellular component: stress fiber;cytoplasm;myosin II complex
• Molecular function: actin binding;myosin II head/neck binding;metal ion binding