FXR1

FMR1 autosomal homolog 1

Basic information

Region (hg38): 3:180868140-180982753

Links

ENSG00000114416 ∙ NCBI:8087 ∙ OMIM:600819 ∙ HGNC:4023 ∙ Uniprot:P51114 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopathy, congenital proximal, with minicore lesions (Limited), mode of inheritance: AR
• myopathy, congenital, with respiratory insufficiency and bone fractures (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital myopathy 9A; Congenital myopathy 9B, proximal, with minicore lesions	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic; Pulmonary	30770808; 35393337

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FXR1 gene.

• not provided (9 variants)
• Inborn genetic diseases (9 variants)
• Congenital myopathy (2 variants)
• Myopathy, congenital, with respiratory insufficiency and bone fractures (1 variants)
• Myopathy, congenital proximal, with minicore lesions;Myopathy, congenital, with respiratory insufficiency and bone fractures (1 variants)
• Delayed gross motor development;Neonatal respiratory distress;Scoliosis (1 variants)
• Multiminicore myopathy (1 variants)
• Myopathy, congenital proximal, with minicore lesions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXR1 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				4	3	7
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	14	5	3

Variants in FXR1

This is a list of pathogenic ClinVar variants found in the FXR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-180912712-C-T			Benign (Aug 15, 2018)
3-180912713-G-T		Myopathy, congenital, with respiratory insufficiency and bone fractures	Uncertain significance (May 02, 2023)
3-180912715-C-T			Likely benign (Dec 01, 2022)
3-180912721-C-T			Likely benign (Jun 01, 2022)
3-180933327-C-T		Myopathy, congenital, with respiratory insufficiency and bone fractures;Myopathy, congenital proximal, with minicore lesions	Benign/Likely benign (Feb 01, 2024)
3-180933362-C-G		Delayed gross motor development;Neonatal respiratory distress;Scoliosis	Uncertain significance (Jan 12, 2022)
3-180933377-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-180947913-A-G		Congenital myopathy	Uncertain significance (Nov 16, 2020)
3-180948422-A-G		Congenital myopathy	Uncertain significance (Nov 16, 2020)
3-180948769-A-T			Benign (Dec 31, 2019)
3-180949288-T-C		not specified	Uncertain significance (Jun 02, 2023)
3-180951305-A-T		not specified	Uncertain significance (Oct 26, 2022)
3-180951420-C-T			Benign/Likely benign (Apr 01, 2024)
3-180961539-T-C			Benign (May 03, 2018)
3-180963044-C-T			Likely benign (Aug 01, 2022)
3-180963079-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-180963084-G-A		not specified	Uncertain significance (Jan 19, 2024)
3-180968159-G-A		not specified	Uncertain significance (Aug 09, 2021)
3-180971082-T-TG		Myopathy, congenital proximal, with minicore lesions	Pathogenic (Mar 13, 2023)
3-180971083-GA-G		Myopathy, congenital proximal, with minicore lesions • Multiminicore myopathy	Uncertain significance (May 28, 2020)
3-180971083-G-GA		Myopathy, congenital proximal, with minicore lesions	Pathogenic (Mar 13, 2023)
3-180971145-TAGAC-T		Myopathy, congenital, with respiratory insufficiency and bone fractures	Pathogenic (Mar 13, 2023)
3-180975394-A-G			Likely benign (Jun 29, 2018)
3-180976147-G-T		not specified	Uncertain significance (Feb 11, 2022)
3-180976152-T-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXR1	protein_coding	protein_coding	ENST00000357559	17	114613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000327	125654	0	3	125657	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.20	182	351	0.519	0.0000194	4068
Missense in Polyphen		56	152.31	0.36768		1715
Synonymous	0.913	101	113	0.891	0.00000587	1170
Loss of Function	5.69	1	39.7	0.0252	0.00000252	429

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)	0.0000183	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs (By similarity). {ECO:0000250}.
• Pathway: RNA transport - Homo sapiens (human);Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.425
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.833
• hipred: Y
• hipred_score: 0.777
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.763

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fxr1
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: fxr1
• Affected structure: skeletal muscle myoblast
• Phenotype tag: abnormal
• Phenotype quality: circular

Gene ontology

• Biological process: apoptotic process;muscle organ development;negative regulation of translation;cell differentiation;regulation of mRNA stability;positive regulation of translation;positive regulation of gene silencing by miRNA
• Cellular component: nucleus;nucleolus;cytoplasm;cytosol;polysome;postsynaptic density;membrane;axon;ribonucleoprotein granule;cytoplasmic ribonucleoprotein granule;neuronal cell body;costamere;dendritic spine;perinuclear region of cytoplasm;glutamatergic synapse
• Molecular function: RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;RNA strand annealing activity;protein homodimerization activity;translation regulator activity;protein heterodimerization activity