NMD3

NMD3 ribosome export adaptor

Basic information

Region (hg38): 3:161104696-161253532

Links

ENSG00000169251

∙ NCBI:51068 ∙ OMIM:611021 ∙ HGNC:24250 ∙ Uniprot:Q96D46 ∙ 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 NMD3 gene.

not_specified (66 variants)
Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015938.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			67 clinvar			67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMD3	protein_coding	protein_coding	ENST00000460469	15	148837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.10e-8	0.988	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.185	260	269	0.968	0.0000137	3342
Missense in Polyphen		66	72.949	0.90474		993
Synonymous	-2.23	114	87.4	1.30	0.00000437	878
Loss of Function	2.34	17	31.1	0.547	0.00000153	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000910
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000220	0.000217
Finnish	0.000372	0.000370
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000220	0.000217
South Asian	0.000196	0.000196
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit. {ECO:0000269|PubMed:12724356, ECO:0000269|PubMed:12773398}.;
Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.108

Intolerance Scores

loftool: 0.860
rvis_EVS: -0.51
rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

pHI: 0.0789
hipred: Y
hipred_score: 0.628
ghis: 0.650

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.556

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nmd3
Phenotype

Zebrafish Information Network

Gene name: nmd3
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: quality

Gene ontology

Biological process: ribosomal large subunit export from nucleus;positive regulation of protein binding;positive regulation of RNA biosynthetic process;positive regulation of protein localization to nucleolus
Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;membrane
Molecular function: RNA binding;protein binding, bridging;ribosomal large subunit binding