MEX3D

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

Basic information

Region (hg38): 19:1554672-1568325

Previous symbols: [ "RKHD1" ]

Links

ENSG00000181588 ∙ NCBI:399664 ∙ OMIM:611009 ∙ HGNC:16734 ∙ Uniprot:Q86XN8 ∙ 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 MEX3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEX3D 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						0
missense			82	4		86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	82	4	0

Variants in MEX3D

This is a list of pathogenic ClinVar variants found in the MEX3D region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1555360-C-T		not specified	Uncertain significance (Nov 26, 2024)
19-1555371-G-T		not specified	Uncertain significance (Dec 23, 2024)
19-1555715-C-T		not specified	Uncertain significance (Mar 26, 2024)
19-1555729-G-A		not specified	Uncertain significance (Sep 12, 2024)
19-1555738-G-A		not specified	Uncertain significance (Aug 09, 2021)
19-1555741-G-A		not specified	Uncertain significance (Oct 20, 2021)
19-1555756-G-T		not specified	Uncertain significance (Oct 10, 2023)
19-1555768-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-1555774-T-G		not specified	Uncertain significance (Jul 25, 2023)
19-1555775-C-G		not specified	Uncertain significance (Sep 27, 2021)
19-1555780-G-T		not specified	Uncertain significance (Jan 18, 2025)
19-1555799-C-G		not specified	Uncertain significance (Jan 30, 2025)
19-1555853-C-T		not specified	Uncertain significance (Nov 14, 2024)
19-1555862-G-A		not specified	Likely benign (Jun 16, 2024)
19-1555909-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-1555924-C-T		not specified	Uncertain significance (May 22, 2023)
19-1555927-C-G		not specified	Uncertain significance (Mar 31, 2022)
19-1555948-C-A		not specified	Uncertain significance (Oct 13, 2023)
19-1555949-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-1555966-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-1555966-G-C		not specified	Uncertain significance (Jul 26, 2021)
19-1555975-G-A		not specified	Uncertain significance (Feb 03, 2022)
19-1555985-G-A		not specified	Uncertain significance (Dec 12, 2024)
19-1555988-G-A		not specified	Uncertain significance (Dec 19, 2022)
19-1555990-G-A		not specified	Uncertain significance (Dec 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEX3D	protein_coding	protein_coding	ENST00000402693	2	13390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.923	0.0766	123360	0	1	123361	0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	153	267	0.574	0.0000201	4005
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000548
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000548	0.0000548
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA binding protein, may be involved in post- transcriptional regulatory mechanisms. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.186
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.282

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mex3d

Gene ontology

• Biological process: mRNA localization resulting in posttranscriptional regulation of gene expression;mRNA destabilization
• Cellular component: nucleus;perinuclear region of cytoplasm
• Molecular function: RNA binding;AU-rich element binding;metal ion binding