MEX3B

protein-coding

mex-3 RNA binding family member B, the group of Ring finger proteins

Gene summary

This gene encodes an RNA-binding phosphoprotein that is part of the MEX3 (muscle excess 3) family of translational regulators. The encoded protein contains N-terminal nuclear export and nuclear localization signals and is exported from the cytoplasm to the nucleus. The protein binds to RNA via two KH domains and also colocalizes with MEX3A, Dcp1A decapping factor and Argonaute proteins within P (processing) bodies. [provided by RefSeq, Oct 2012]

Previous symbols:

RKHD3

MANE transcript

NM_032246.6

Inheritance

—

ClinVar variants

U:91B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr15:82,041,778-82,046,119

External References & Databases

Ensembl (ENSG00000183496)

Transcript & Mutation Effects

hg38 • Region Span ~4.3 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 MEX3B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032246.6. 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			1 clinvar	2 clinvar		3
missense			90 clinvar	1 clinvar		91
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	91	3	0	94

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032246.6	RefSeq	NP_115622.2	2	MANE Select
ENST00000329713.5	Ensembl	ENSP00000329918.4	2	MANE Select
ENST00000558133.1	Ensembl	ENSP00000456938.1	1	Standard
ENST00001137151.1	Ensembl	ENSP00000807230.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
protein autophosphorylation

Molecular Function

RNA binding
calcium ion binding

Cellular Component

P-body
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329713
Coding exons: 2
Length: 4364
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125743
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	298	354	0.842	0.0000204	3599
Missense (PolyPhen)		48	110.96	0.43258		1088
Synonymous	-4.06	229	163	1.40	0.0000105	1259
Loss of Function	2.51	2	11.0	0.182	4.70e-7	129

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA-binding protein. May be involved in post- transcriptional regulatory mechanisms.;

Recessive Scores

pRec: 0.111

Intolerance Scores

RVIS EVS: -0.76
RVIS percentile EVS: 13.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.920

Gene Damage Prediction

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