FXR2

protein-coding

FMR1 autosomal homolog 2

Gene summary

The protein encoded by this gene is a RNA binding protein containing two KH domains and one RCG box, which is similar to FMRP and FXR1. It associates with polyribosomes, predominantly with 60S large ribosomal subunits. This encoded protein may self-associate or interact with FMRP and FXR1. It may have a role in the development of fragile X cognitive disability syndrome. [provided by RefSeq, Jul 2008]

Previous symbols:

FMR1L2

MANE transcript

NM_004860.4

Inheritance

—

ClinVar variants

U:89B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr17:7,591,230-7,614,897

External References & Databases

Ensembl (ENSG00000129245)

Transcript & Mutation Effects

hg38 • Region Span ~23.7 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 FXR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004860.4. 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				2 clinvar	1 clinvar	3
missense			87 clinvar	2 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	89	4	1	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004860.4	RefSeq	NP_004851.2	17	MANE Select
ENST00000250113.12	Ensembl	ENSP00000250113.7	17	MANE Select
ENST00000571597.1	Ensembl	ENSP00000459230.1	5	Standard
ENST00000704984.1	Ensembl	ENSP00000516064.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)
miR-targeted genes in lymphocytes - TarBase

Biological Process

negative regulation of translation
regulation of mRNA stability
positive regulation of translation

Molecular Function

RNA binding
mRNA binding
mRNA 3'-UTR binding
protein binding
identical protein binding

Cellular Component

nucleus
cytoplasm
cytosol
polysome
postsynaptic density

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000250113
Coding exons: 17
Length: 23642
Individuals with no LoFs: 124637
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124639
p: 0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.62	258	407	0.634	0.0000257	4281
Missense (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

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)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein.;

Recessive Scores

pRec: 0.149

Intolerance Scores

RVIS EVS: -0.53
RVIS percentile EVS: 20.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.591

Gene Damage Prediction

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