NSUN4

NOP2/Sun RNA methyltransferase 4, the group of NOP2/Sun RNA methyltransferase family

Basic information

Region (hg38): 1:46340789-46369218

Links

ENSG00000117481 ∙ NCBI:387338 ∙ OMIM:615394 ∙ HGNC:31802 ∙ Uniprot:Q96CB9 ∙ 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 NSUN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSUN4 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 NSUN4

This is a list of pathogenic ClinVar variants found in the NSUN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46340870-G-A		not specified	Uncertain significance (Apr 21, 2022)
1-46340876-A-G		not specified	Uncertain significance (May 05, 2023)
1-46340891-C-G		not specified	Uncertain significance (Mar 28, 2023)
1-46344881-T-A		not specified	Uncertain significance (Nov 13, 2023)
1-46345057-C-A		not specified	Uncertain significance (Jan 02, 2024)
1-46345084-G-T		not specified	Uncertain significance (Jan 11, 2023)
1-46345117-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-46345138-C-A		not specified	Uncertain significance (Nov 07, 2022)
1-46346991-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-46352895-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-46352909-A-G		not specified	Uncertain significance (Apr 24, 2023)
1-46352936-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-46352970-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-46360734-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-46361590-A-G		not specified	Uncertain significance (Sep 23, 2023)
1-46361602-A-G		not specified	Uncertain significance (Jun 18, 2021)
1-46361625-C-T		not specified	Uncertain significance (Aug 10, 2021)
1-46361643-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-46361725-G-A		not specified	Uncertain significance (Jun 13, 2023)
1-46361823-T-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSUN4	protein_coding	protein_coding	ENST00000474844	6	24976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000123	0.951	125512	0	235	125747	0.000935

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.832	183	218	0.841	0.0000113	2463
Missense in Polyphen		72	82.677	0.87086		935
Synonymous	1.03	72	84.0	0.857	0.00000415	795
Loss of Function	1.87	13	22.6	0.575	0.00000162	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00282	0.00281
Ashkenazi Jewish	0.00341	0.00338
East Asian	0.000652	0.000653
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000449	0.000448
Middle Eastern	0.000652	0.000653
South Asian	0.00209	0.00209
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in mitochondrial ribosome assembly. 5- methylcytosine rRNA methyltransferase that probably is involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA; the function is independent of MTERFD2/MTERF4 and assembled mitochondrial ribosome large subunit (LSU). Targeted to LSU by MTERFD2/MTERF4 and probably is involved in a final step in ribosome biogenesis to ensure that SSU and LSU are assembled. In vitro can methylate 16S rRNA of the LSU; the methylation is enhanced by MTERFD/MTERF4. {ECO:0000269|PubMed:21531335, ECO:0000269|PubMed:23022348}.
• Pathway: rRNA processing;rRNA modification in the mitochondrion;Metabolism of RNA;rRNA processing in the mitochondrion (Consensus)

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.906
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.0730
• hipred: N
• hipred_score: 0.197
• ghis: 0.487

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Nsun4

Gene ontology

• Biological process: rRNA methylation;mature ribosome assembly;positive regulation of mitochondrial translation
• Cellular component: mitochondrial matrix;mitochondrial large ribosomal subunit
• Molecular function: protein binding;methyltransferase activity;rRNA (cytosine-C5-)-methyltransferase activity;small ribosomal subunit rRNA binding