FHL1
protein-codingfour and a half LIM domains 1, the group of LIM domain containing
Gene summary
This gene encodes a member of the four-and-a-half-LIM-only protein family. Family members contain two highly conserved, tandemly arranged, zinc finger domains with four highly conserved cysteines binding a zinc atom in each zinc finger. Expression of these family members occurs in a cell- and tissue-specific mode and these proteins are involved in many cellular processes. Mutations in this gene have been found in patients with Emery-Dreifuss muscular dystrophy. Multiple alternately spliced transcript variants which encode different protein isoforms have been described.[provided by RefSeq, Nov 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~64.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0019948
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010680
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010400
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010401
Submitter: Orphanet
Inheritance Pattern: XL
Disease ID:MONDO:0010401
Submitter: G2P
Inheritance Pattern: XL
Disease ID:MONDO:0800462
Submitter: PanelApp Australia
Inheritance Pattern: XL
Disease ID:MONDO:0010401
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XL
Disease ID:MONDO:0010414
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: Surveillance for cardiovascular disease (eg, cardiomyopathy, arrhythmias) and early medical treatment may reduce morbidity
Comments: In reducing body myopathy, dilated cardiomyopathy has been described, but well after clinical onset; In Myopathy with postural muscle atrophy and Emery-Dreifuss muscular dystrophy 6, heart failure can be deadly, perhaps related to hypertrophic cardiomyopathy; In Emery-Dreifuss muscular dystrophy 6, arrhythmias have been desribed, as well as sudden cardiac death; In all situations, survelliance and early medical management could be beneficial, but the condition may not be easily clinically recognizable
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FHL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001159699.2. 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 | 10 | 114 | 124 | |||
| missense | 14 | 18 | 245 | 14 | 291 | |
| nonsense | 13 | 9 | 7 | 29 | ||
| start loss | 1 | 1 | ||||
| frameshift | 36 | 9 | 2 | 47 | ||
| splice donor/acceptor (+/-2bp) | 7 | 3 | 13 | 23 | ||
| Total | 70 | 39 | 278 | 128 | 0 | 515 |
Highest pathogenic variant AF is 0.000009043472
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001153171.1 | 6 | MANE Select | |
| Ensembl | ENSP00000359717.1 | 6 | MANE Select | |
| RefSeq | NP_001153172.1 | 5 | Standard | |
| RefSeq | NP_001153173.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| fhl1a | Danio rerio | Structure: skeletal muscle Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Jak-STAT signaling pathway - Homo sapiens (human)
- Notch Signaling Pathway
- Notch
Biological Process
- regulation of membrane depolarization
- muscle organ development
- animal organ morphogenesis
- negative regulation of G2/M transition of mitotic cell cycle
- cell differentiation
Molecular Function
- molecular_function
- protein binding
- ion channel binding
- metal ion binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
- plasma membrane
- focal adhesion
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394155
- Coding exons
- 6
- Length
- 63960
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.890 | 105 | 134 | 0.784 | 0.0000108 | 2144 |
| Missense (PolyPhen) | 27 | 45.938 | 0.58774 | 803 | ||
| Synonymous | 1.32 | 40 | 52.1 | 0.767 | 0.00000445 | 586 |
| Loss of Function | 3.05 | 0 | 10.8 | 0.00 | 7.62e-7 | 196 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May have an involvement in muscle development or hypertrophy.;
- Disease
- DISEASE: Emery-Dreifuss muscular dystrophy 6, X-linked (EDMD6) [MIM:300696]: A form of Emery-Dreifuss muscular dystrophy, a degenerative myopathy characterized by weakness and atrophy of muscle without involvement of the nervous system, early contractures of the elbows, Achilles tendons and spine, and cardiomyopathy associated with cardiac conduction defects. {ECO:0000269|PubMed:19716112, ECO:0000269|PubMed:20186852}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry.; DISEASE: Scapuloperoneal myopathy, X-linked dominant (SPM) [MIM:300695]: A disease characterized by progressive muscle weakness and wasting, upper and lower limbs weakness, foot drop, scapular winging, and myopathic changes on muscle biopsy. Most affected individuals become wheelchair-bound. {ECO:0000269|PubMed:18179901, ECO:0000269|PubMed:27234031}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myopathy, X-linked, with postural muscle atrophy (XMPMA) [MIM:300696]: A progressive muscular dystrophy with onset in adulthood. Affected individuals develop a proximal myopathy characterized by specific atrophy of postural muscles, limited neck flexion, bent spine, contractures of the Achilles tendon, respiratory problems, and cardiomyopathy. Patients may show muscle hypertrophy in the early stages of the disorder. {ECO:0000269|PubMed:18179888, ECO:0000269|PubMed:19687455}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reducing body myopathy, X-linked 1A, severe, with infantile or early childhood onset (RBMX1A) [MIM:300717]: A rare myopathy clinically characterized by rapidly progressive muscular weakness, and pathologically by the presence of intracytoplasmic inclusion bodies strongly stained by menadione-linked alpha- glycerophosphate dehydrogenase in the absence of substrate, alpha- glycerophosphate. The term 'reducing body' refers to the reducing activity of the inclusions to nitroblue tetrazolium in the absence of substrate. This condition is also commonly associated with rimmed vacuoles and cytoplasmic bodies. Death in childhood is frequent in the severe form of the disease, due to respiratory failure. {ECO:0000269|PubMed:18274675, ECO:0000269|PubMed:19171836, ECO:0000269|PubMed:19181672}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reducing body myopathy, X-linked 1B, with late childhood or adult onset (RBMX1B) [MIM:300718]: A rare myopathy clinically characterized by rapidly progressive muscular weakness, and pathologically by the presence of intracytoplasmic inclusion bodies strongly stained by menadione-linked alpha-glycerophosphate dehydrogenase in the absence of substrate, alpha-glycerophosphate. The term 'reducing body' refers to the reducing activity of the inclusions to nitroblue tetrazolium in the absence of substrate. This condition is also commonly associated with rimmed vacuoles and cytoplasmic bodies. {ECO:0000269|PubMed:18274675, ECO:0000269|PubMed:19171836, ECO:0000269|PubMed:19181672, ECO:0000269|PubMed:23169582}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Uruguay faciocardiomusculoskeletal syndrome (FCMSU) [MIM:300280]: A X-linked recessive syndrome characterized by brachyturricephaly, pugilistic coarse facies, a muffled voice, cardiomyopathy, muscular hypertrophy, broad hands, wide feet with progressive pes cavus deformities, dislocation of toes, variable congenital hip dislocation, and scoliosis. {ECO:0000269|PubMed:26933038}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.4
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |