MEX3D

protein-coding

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

Gene summary

Enables mRNA 3'-UTR AU-rich region binding activity. Predicted to be involved in mRNA destabilization and mRNA localization resulting in post-transcriptional regulation of gene expression. Located in nucleus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

RKHD1

MANE transcript

NM_203304.4

Inheritance

—

ClinVar variants

U:148B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:1,554,672-1,568,325

External References & Databases

Ensembl (ENSG00000181588)

Transcript & Mutation Effects

hg38 • Region Span ~13.7 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 MEX3D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 151

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203304.4. 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			1 clinvar			1
missense			146 clinvar	6 clinvar		152
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	148	6	0	154

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203304.4	RefSeq	NP_976049.3	2	MANE Select
ENST00000402693.5	Ensembl	ENSP00000384398.3	2	MANE Select
NM_001174118.2	RefSeq	NP_001167589.1	3	Standard
ENST00000605173.2	Ensembl	ENSP00000475059.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA localization resulting in posttranscriptional regulation of gene expression
mRNA destabilization

Molecular Function

RNA binding
AU-rich element binding
metal ion binding

Cellular Component

nucleus
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000402693
Coding exons: 2
Length: 13390
Individuals with no LoFs: 123360
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 123361
p: 0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.47	153	267	0.574	0.0000201	4005
Missense (PolyPhen)		52	128.84	0.4036		1234
Synonymous	-0.858	153	140	1.09	0.0000130	1519
Loss of Function	2.65	0	8.21	0.00	4.89e-7	112

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	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
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. {ECO:0000250}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.282

Gene Damage Prediction

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