GeneBe

NSUN6

NOP2/Sun RNA methyltransferase 6, the group of NOP2/Sun RNA methyltransferase family

Basic information

Region (hg38): 10:18545561-18659285

Previous symbols: [ "NOPD1", "ARL5B-AS1" ]

Links

ENSG00000241058 ∙ NCBI:221078 ∙ OMIM:617199 ∙ HGNC:23529 ∙ Uniprot:Q8TEA1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Intellectual developmental disorder, autosomal recessive 82ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic37226891

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NSUN6 gene.

  • not_specified (65 variants)
  • Intellectual_developmental_disorder,_autosomal_recessive_82 (3 variants)
  • not_provided (2 variants)
  • Developmental_and_epileptic_encephalopathy,_83 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSUN6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000182543.5. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
1
clinvar
64
clinvar
2
clinvar
 67
nonsense
0
start loss
0
frameshift
1
clinvar
1
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total 2 0 65 2 0

Highest pathogenic variant AF is 0.00012887998

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NSUN6protein_codingprotein_codingENST00000377304 11106062
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.95e-190.0015712555601901257460.000756
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.332922351.240.00001123029
Missense in Polyphen9879.2761.2362978
Synonymous-1.4110285.51.190.00000412908
Loss of Function-0.3392725.21.070.00000131325

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003030.00297
Ashkenazi Jewish0.002380.00238
East Asian0.001870.00185
Finnish0.0003240.000323
European (Non-Finnish)0.0004210.000413
Middle Eastern0.001870.00185
South Asian0.0005540.000523
Other0.0008230.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: May have S-adenosyl-L-methionine-dependent methyl- transferase activity. {ECO:0000305}.;
Pathway
tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

pRec
0.0991

Intolerance Scores

loftool
0.729
rvis_EVS
-0.2
rvis_percentile_EVS
38.98

Haploinsufficiency Scores

pHI
0.979
hipred
N
hipred_score
0.477
ghis
0.584

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.159

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nsun6
Phenotype

Gene ontology

Biological process
tRNA modification;tRNA methylation
Cellular component
cytoplasm;cytosol
Molecular function
tRNA binding;tRNA (cytosine-5-)-methyltransferase activity