NSUN5

NOP2/Sun RNA methyltransferase 5, the group of NOP2/Sun RNA methyltransferase family

Basic information

Region (hg38): 7:73302516-73308826

Previous symbols: [ "WBSCR20", "WBSCR20A" ]

Links

ENSG00000130305

∙ NCBI:55695 ∙ OMIM:615732 ∙ HGNC:16385 ∙ Uniprot:Q96P11 ∙ 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 NSUN5 gene.

not_specified (82 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSUN5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000148956.4. 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			3 clinvar	2 clinvar		5
missense			66 clinvar	11 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	69	13	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSUN5	protein_coding	protein_coding	ENST00000310326	10	6351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.24e-13	0.0718	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.175	291	300	0.972	0.0000185	2990
Missense in Polyphen		94	99.675	0.94307		1061
Synonymous	-0.742	144	133	1.08	0.00000802	1026
Loss of Function	0.466	20	22.4	0.894	0.00000136	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000836	0.000834
Ashkenazi Jewish	0.00310	0.00308
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.000273	0.000272
South Asian	0.000425	0.000425
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C(5) position of cytosine 3782 in 28S rRNA. {ECO:0000305|PubMed:23913415}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.914
rvis_EVS: 0.02
rvis_percentile_EVS: 55.76

Haploinsufficiency Scores

pHI: 0.871
hipred: N
hipred_score: 0.213
ghis: 0.506

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.770

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nsun5
Phenotype

Gene ontology

Biological process: rRNA base methylation
Cellular component: nucleus;nucleolus
Molecular function: RNA binding;methyltransferase activity