FHL1

protein-coding

four 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

NM_001159699.2

Inheritance

XL

ClinVar variants

P:109U:278B:128

Top phenotype

Reducing body myopathy, X-linked 1A, with infantile or early childhood onset; Reducing body myopathy, X-linked 1B, with late childhood or adult onset; Emery-Dreifuss muscular dystrophy 6, X-linked; Myopathy, X-linked, with postural muscle atrophy; Uruguay faciocardiomusculoskeletal syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:136,146,702-136,211,359

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~64.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

reducing body myopathySUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0019948

Submitter: Orphanet

X-linked Emery-Dreifuss muscular dystrophySUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010680

Submitter: Orphanet

X-linked scapuloperoneal muscular dystrophySUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010400

Submitter: Orphanet

X-linked myopathy with postural muscle atrophySUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010401

Submitter: Orphanet

X-linked myopathy with postural muscle atrophyDEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010401

Submitter: G2P

FHL1-related myopathySTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0800462

Submitter: PanelApp Australia

X-linked myopathy with postural muscle atrophySTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010401

Submitter: Labcorp Genetics (formerly Invitae)

myopathy, reducing body, X-linked, early-onset, severeSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010414

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Reducing body myopathy, X-linked 1A, with infantile or early childhood onset; Reducing body myopathy, X-linked 1B, with late childhood or adult onset; Emery-Dreifuss muscular dystrophy 6, X-linked; Myopathy, X-linked, with postural muscle atrophy; Uruguay faciocardiomusculoskeletal syndromeXL

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

Refs: 4250729; 7722535; 8619529; 11102932; 16919903; 18179901; 18952429; 18274675; 18179888; 19716112; 19181672; 19687455; 19171836; 20186852; 26933038Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FHL1 variants in ClinVar

21 Conditions Cataloged
X-linked myopathy with postural muscle atrophyTotal: 463
Cardiovascular phenotypeTotal: 161
not providedTotal: 158
not specifiedTotal: 70
FHL1-related disorderTotal: 42
Myopathy, reducing body, X-linked, early-onset, severeTotal: 29
X-linked scapuloperoneal muscular dystrophyTotal: 28
Myopathy, reducing body, X-linked, childhood-onsetTotal: 27

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
114
clinvar
124
missense
14
clinvar
18
clinvar
245
clinvar
14
clinvar
291
nonsense
13
clinvar
9
clinvar
7
clinvar
29
start loss
1
clinvar
1
frameshift
36
clinvar
9
clinvar
2
clinvar
47
splice donor/acceptor (+/-2bp)
7
clinvar
3
clinvar
13
clinvar
23
Total70392781280515

Highest pathogenic variant AF is 0.000009043472

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001159699.2RefSeqNP_001153171.16MANE Select
ENST00000370683.6EnsemblENSP00000359717.16MANE Select
NM_001159700.2RefSeqNP_001153172.15Standard
NM_001159701.2RefSeqNP_001153173.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
fhl1aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8901051340.7840.00001082144
Missense (PolyPhen)2745.9380.58774803
Synonymous1.324052.10.7670.00000445586
Loss of Function3.05010.80.007.62e-7196

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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