NMD3

NMD3 ribosome export adaptor

Basic information

Region (hg38): 3:161104695-161253532

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.

• Inborn genetic diseases (19 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.

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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in NMD3

This is a list of pathogenic ClinVar variants found in the NMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-161224955-A-G		not specified	Uncertain significance (Mar 24, 2023)
3-161233412-A-G		not specified	Uncertain significance (Dec 13, 2022)
3-161234750-A-T		not specified	Uncertain significance (Jan 24, 2023)
3-161235138-C-T		Malignant tumor of prostate	Uncertain significance (-)
3-161235178-G-A		not specified	Uncertain significance (Jul 19, 2022)
3-161235195-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-161238759-A-G		not specified	Uncertain significance (Jun 29, 2023)
3-161241119-G-A		not specified	Uncertain significance (Oct 20, 2023)
3-161241154-A-G		not specified	Uncertain significance (May 05, 2023)
3-161242543-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-161242589-T-G		not specified	Uncertain significance (Jan 18, 2022)
3-161242601-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-161242616-T-C		not specified	Uncertain significance (Jul 27, 2021)
3-161242621-C-T		not specified	Uncertain significance (Jun 02, 2023)
3-161246345-G-A		not specified	Uncertain significance (Dec 19, 2023)
3-161246400-G-C		not specified	Uncertain significance (Jun 22, 2023)
3-161246403-G-C		not specified	Uncertain significance (Mar 01, 2023)
3-161246432-G-A		not specified	Uncertain significance (Aug 05, 2023)
3-161246435-G-C		not specified	Uncertain significance (Nov 03, 2022)
3-161249478-C-T		not specified	Uncertain significance (Feb 13, 2024)
3-161249479-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-161249488-G-A		not specified	Uncertain significance (Dec 27, 2023)
3-161249493-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-161249532-A-G		not specified	Uncertain significance (May 15, 2023)
3-161249548-C-T		not specified	Uncertain significance (Aug 12, 2021)

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

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