FXR2

FMR1 autosomal homolog 2

Basic information

Region (hg38): 17:7591229-7614897

Previous symbols: [ "FMR1L2" ]

Links

ENSG00000129245 ∙ NCBI:9513 ∙ OMIM:605339 ∙ HGNC:4024 ∙ Uniprot:P51116 ∙ 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 FXR2 gene.

• Inborn genetic diseases (29 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXR2 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	1	3
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	4	1

Variants in FXR2

This is a list of pathogenic ClinVar variants found in the FXR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7591891-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-7591901-T-C			Likely benign (Jul 31, 2018)
17-7592268-G-C		not specified	Uncertain significance (Sep 01, 2021)
17-7592282-G-A		not specified	Uncertain significance (Jan 24, 2023)
17-7592342-T-C		not specified	Uncertain significance (Mar 23, 2022)
17-7592349-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-7592525-T-C		not specified	Uncertain significance (Jun 29, 2023)
17-7592533-T-A		not specified	Uncertain significance (Oct 25, 2023)
17-7592542-T-C		not specified	Uncertain significance (Oct 22, 2021)
17-7592580-T-A		not specified	Uncertain significance (Dec 28, 2022)
17-7592696-A-G		not specified	Uncertain significance (Jan 31, 2024)
17-7592738-C-G		not specified	Uncertain significance (Feb 07, 2023)
17-7592741-T-C		not specified	Uncertain significance (Dec 15, 2023)
17-7592777-C-T		not specified	Uncertain significance (Nov 18, 2022)
17-7592778-G-A		not specified	Uncertain significance (May 23, 2023)
17-7592786-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-7592805-G-T		not specified	Uncertain significance (Feb 16, 2023)
17-7592810-G-A		not specified	Uncertain significance (Nov 29, 2023)
17-7592810-G-C		not specified	Uncertain significance (Jun 21, 2023)
17-7592834-G-A		not specified	Uncertain significance (Feb 03, 2022)
17-7593022-C-T		not specified	Uncertain significance (Mar 29, 2022)
17-7593023-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-7593056-C-T		not specified	Uncertain significance (Jul 26, 2021)
17-7593064-C-T			Likely benign (Jun 08, 2018)
17-7593073-C-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FXR2	protein_coding	protein_coding	ENST00000250113	17	23642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000381	124637	0	2	124639	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	258	407	0.634	0.0000257	4281
Missense in Polyphen		85	182.33	0.46619		1727
Synonymous	0.416	140	146	0.956	0.00000778	1382
Loss of Function	5.58	3	42.0	0.0715	0.00000287	412

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)	0.00000887	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein.
• Pathway: RNA transport - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.411
• hipred: Y
• hipred_score: 0.576
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fxr2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of translation;regulation of mRNA stability;positive regulation of translation
• Cellular component: nucleus;cytoplasm;cytosol;polysome;postsynaptic density;membrane;cytosolic large ribosomal subunit;axon;ribonucleoprotein granule;cytoplasmic ribonucleoprotein granule;neuronal cell body;dendritic spine
• Molecular function: RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;identical protein binding;protein homodimerization activity;translation regulator activity;protein heterodimerization activity