NSA2

NSA2 ribosome biogenesis factor, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 5:74766990-74780113

Links

ENSG00000164346 ∙ NCBI:10412 ∙ OMIM:612497 ∙ HGNC:30728 ∙ Uniprot:O95478 ∙ 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 NSA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSA2 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	10	0	3

Variants in NSA2

This is a list of pathogenic ClinVar variants found in the NSA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-74767056-C-T			Benign (Jun 29, 2018)
5-74767244-G-A			Benign (Jun 24, 2021)
5-74767329-C-G			Benign (Jun 29, 2018)
5-74767425-T-C			Benign (Jun 23, 2018)
5-74767443-G-T			Benign (Jun 23, 2018)
5-74769242-A-G		not specified	Uncertain significance (Jun 07, 2024)
5-74769264-C-T		not specified	Uncertain significance (Aug 23, 2021)
5-74769308-C-A		not specified	Uncertain significance (Apr 25, 2023)
5-74770664-G-T		not specified	Uncertain significance (Jun 26, 2023)
5-74770683-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-74770698-G-A		not specified	Uncertain significance (Nov 30, 2022)
5-74770718-A-G		not specified	Uncertain significance (Nov 30, 2022)
5-74770798-C-A		not specified	Uncertain significance (Jun 03, 2022)
5-74770804-G-C		not specified	Uncertain significance (Aug 08, 2022)
5-74773872-T-G		not specified	Uncertain significance (Sep 14, 2023)
5-74773973-A-T		not specified	Uncertain significance (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSA2	protein_coding	protein_coding	ENST00000296802	6	9921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.981	125714	0	28	125742	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.770	116	142	0.818	0.00000776	1686
Missense in Polyphen		14	19.854	0.70516		312
Synonymous	1.20	34	44.1	0.771	0.00000198	477
Loss of Function	2.29	6	15.8	0.379	9.55e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000170	0.000158
Middle Eastern	0.000111	0.000109
South Asian	0.0000357	0.0000327
Other	0.000350	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.770
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.783
• ghis: 0.660

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsa2

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleolus;preribosome, large subunit precursor
• Molecular function: RNA binding