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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 82	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	37226891

ClinVar

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

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.

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			32	2		34
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in NSUN6

This is a list of pathogenic ClinVar variants found in the NSUN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-18545948-T-G		not specified	Uncertain significance (Apr 05, 2023)
10-18545953-C-A		not specified	Uncertain significance (Apr 15, 2024)
10-18545971-A-G		not specified	Uncertain significance (Nov 21, 2023)
10-18545977-T-C		not specified	Uncertain significance (Dec 13, 2023)
10-18545992-C-T		not specified	Uncertain significance (Oct 10, 2023)
10-18546019-CCTCT-C		Intellectual developmental disorder, autosomal recessive 82	Pathogenic (Apr 10, 2024)
10-18546063-G-A		not specified	Uncertain significance (Dec 19, 2023)
10-18546097-C-G		not specified	Uncertain significance (Mar 21, 2023)
10-18546120-A-C		not specified	Uncertain significance (Apr 25, 2023)
10-18546134-A-C		not specified	Uncertain significance (Apr 25, 2022)
10-18548116-G-C		not specified	Uncertain significance (Dec 27, 2022)
10-18548118-C-A		not specified	Uncertain significance (Dec 14, 2021)
10-18548161-T-C		not specified	Uncertain significance (Sep 01, 2021)
10-18548180-G-C		not specified	Uncertain significance (Oct 06, 2023)
10-18551824-G-A		not specified	Likely benign (Apr 27, 2022)
10-18551839-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-18551897-G-A		not specified	Uncertain significance (Mar 20, 2024)
10-18551927-C-T		Intellectual developmental disorder, autosomal recessive 82	Pathogenic (Apr 10, 2024)
10-18585970-C-T		not specified	Uncertain significance (Feb 12, 2024)
10-18585990-C-G		not specified	Uncertain significance (Aug 13, 2021)
10-18586003-A-G		not specified	Uncertain significance (Feb 06, 2023)
10-18586005-G-T		not specified	Uncertain significance (Dec 11, 2023)
10-18586060-T-C		not specified	Uncertain significance (Aug 30, 2021)
10-18609861-C-T		not specified	Uncertain significance (Aug 09, 2021)
10-18609874-T-C		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSUN6	protein_coding	protein_coding	ENST00000377304	11	106062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.95e-19	0.00157	125556	0	190	125746	0.000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.33	292	235	1.24	0.0000112	3029
Missense in Polyphen		98	79.276	1.2362		978
Synonymous	-1.41	102	85.5	1.19	0.00000412	908
Loss of Function	-0.339	27	25.2	1.07	0.00000131	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00303	0.00297
Ashkenazi Jewish	0.00238	0.00238
East Asian	0.00187	0.00185
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000421	0.000413
Middle Eastern	0.00187	0.00185
South Asian	0.000554	0.000523
Other	0.000823	0.000815

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

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

Mouse Genome Informatics

• Gene name: Nsun6

Gene ontology

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