NSUN7

NOP2/Sun RNA methyltransferase family member 7, the group of NOP2/Sun RNA methyltransferase family

Basic information

Region (hg38): 4:40749925-40811184

Links

ENSG00000179299 ∙ NCBI:79730 ∙ OMIM:617185 ∙ HGNC:25857 ∙ Uniprot:Q8NE18 ∙ 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 NSUN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSUN7 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			59	3		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	59	3	0

Variants in NSUN7

This is a list of pathogenic ClinVar variants found in the NSUN7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-40750698-T-C		not specified	Uncertain significance (Aug 17, 2022)
4-40750703-T-A		not specified	Uncertain significance (Nov 13, 2024)
4-40750704-C-T		not specified	Uncertain significance (Nov 13, 2024)
4-40750718-G-A		not specified	Uncertain significance (Dec 01, 2023)
4-40750740-C-T		not specified	Uncertain significance (Feb 15, 2023)
4-40750752-C-T		not specified	Uncertain significance (Apr 28, 2022)
4-40750818-A-G		not specified	Uncertain significance (May 16, 2023)
4-40750824-A-G		not specified	Uncertain significance (Mar 01, 2025)
4-40750859-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-40750870-C-G		not specified	Uncertain significance (Jan 17, 2025)
4-40750913-C-T		not specified	Uncertain significance (Aug 27, 2024)
4-40750931-G-A		not specified	Uncertain significance (Sep 29, 2022)
4-40760443-T-C		not specified	Uncertain significance (Jun 04, 2024)
4-40760448-G-A		not specified	Uncertain significance (Dec 03, 2024)
4-40760466-A-T		not specified	Uncertain significance (Dec 27, 2023)
4-40761221-T-G		not specified	Uncertain significance (Feb 05, 2025)
4-40761237-C-T		not specified	Uncertain significance (Feb 07, 2025)
4-40761238-G-A		not specified	Uncertain significance (Feb 09, 2023)
4-40761265-T-A		not specified	Uncertain significance (Mar 01, 2023)
4-40774303-G-A		not specified	Uncertain significance (Sep 20, 2023)
4-40774312-A-G		not specified	Uncertain significance (Sep 30, 2024)
4-40774392-G-A		not specified	Uncertain significance (Mar 11, 2024)
4-40774398-A-G		not specified	Uncertain significance (Jun 30, 2022)
4-40774408-G-A		not specified	Uncertain significance (Jan 02, 2025)
4-40774804-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSUN7	protein_coding	protein_coding	ENST00000381782	11	60089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000479	0.992	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.476	341	367	0.930	0.0000179	4672
Missense in Polyphen		70	82.166	0.85193		1120
Synonymous	1.62	108	132	0.820	0.00000598	1421
Loss of Function	2.38	13	26.1	0.497	0.00000131	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000402	0.000401
Ashkenazi Jewish	0.00	0.00
East Asian	0.000338	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000338	0.000326
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have S-adenosyl-L-methionine-dependent methyl- transferase activity. {ECO:0000305}.

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.4

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: N
• hipred_score: 0.266
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0296

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsun7
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: methylation
• Molecular function: RNA binding;methyltransferase activity