NSUN7

protein-coding

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

Gene summary

Predicted to enable RNA binding activity and methyltransferase activity. Predicted to be involved in methylation. Predicted to act upstream of or within flagellated sperm motility and sperm mitochondrion organization. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_024677.6

Inheritance

—

ClinVar variants

U:102B:4

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr4:40,749,925-40,811,184

External References & Databases

Ensembl (ENSG00000179299)

Transcript & Mutation Effects

hg38 • Region Span ~61.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NSUN7 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024677.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			100 clinvar	4 clinvar		104
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	4	0	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024677.6	RefSeq	NP_078953.4	11	MANE Select
ENST00000381782.7	Ensembl	ENSP00000371201.2	11	MANE Select
NM_001330648.3	RefSeq	NP_001317577.1	10	Standard
ENST00000316607.5	Ensembl	ENSP00000319127.5	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

methylation

Molecular Function

RNA binding
methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381782
Coding exons: 11
Length: 60089
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.476	341	367	0.930	0.0000179	4672
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00022	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0296

Gene Damage Prediction

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