LIMCH1

protein-coding

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

Gene summary

Enables myosin II head/neck binding activity. Involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Located in myosin II complex and stress fiber. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001330672.2

Inheritance

—

ClinVar variants

U:169B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr4:41,359,607-41,700,044

External References & Databases

Ensembl (ENSG00000064042)

Transcript & Mutation Effects

hg38 • Region Span ~340.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LIMCH1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 153

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330672.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			153 clinvar	9 clinvar		162
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			11 clinvar	1 clinvar		12
Total	0	0	169	12	0	181

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 398 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330672.2	RefSeq	NP_001317601.1	29	MANE Select
ENST00000503057.6	Ensembl	ENSP00000425631.1	29	MANE Select
NM_001112717.4	RefSeq	NP_001106188.1	26	Standard
NM_001112718.4	RefSeq	NP_001106189.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

actin binding
myosin II head/neck binding
metal ion binding

Cellular Component

stress fiber
cytoplasm
myosin II complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313860
Coding exons: 27
Length: 340438
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 125748
p: 0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.523	564	600	0.940	0.0000338	7104
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00081	0.00080	rare
Latino/Admixed American	0.0022	0.0022	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0923

Gene Damage Prediction

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