SUPV3L1

protein-coding

Suv3 like RNA helicase, the group of RNA helicases

Gene summary

Enables several functions, including double-stranded RNA binding activity; helicase activity; and protein homodimerization activity. Contributes to 3'-5'-RNA exonuclease activity. Involved in several processes, including mitochondrial RNA metabolic process; positive regulation of cell growth; and positive regulation of mitochondrial RNA catabolic process. Located in mitochondrial nucleoid and nucleus. Part of mitochondrial degradosome. Is active in mitochondrial matrix. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_003171.5

Inheritance

—

ClinVar variants

U:104B:7

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr10:69,180,234-69,209,099

External References & Databases

Ensembl (ENSG00000156502)

Transcript & Mutation Effects

hg38 • Region Span ~28.9 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 SUPV3L1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003171.5. 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	2 clinvar		3
missense			100 clinvar	5 clinvar		105
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	104	7	0	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003171.5	RefSeq	NP_003162.2	15	MANE Select
ENST00000359655.9	Ensembl	ENSP00000352678.4	15	MANE Select
NM_001301683.2	RefSeq	NP_001288612.1	13	Standard
NM_001323584.2	RefSeq	NP_001310513.1	13	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
supv3l1	Danio rerio	Structure: hepatocyte Quality: disorganized abnormal

Gene / Model

Organism

Observed Phenotype

supv3l1

Danio rerio

Structure: hepatocyte

Quality: disorganized

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mitochondrial mRNA catabolic process
positive regulation of mitochondrial RNA catabolic process
mitochondrial RNA 3'-end processing
DNA recombination
RNA catabolic process

Molecular Function

DNA binding
DNA helicase activity
RNA binding
double-stranded RNA binding
ATP-dependent RNA helicase activity

Cellular Component

nucleus
mitochondrion
mitochondrial matrix
mitochondrial nucleoid
mitochondrial degradosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359655
Coding exons: 15
Length: 28868
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125747
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.15	364	431	0.845	0.0000215	5157
Missense (PolyPhen)		78	139.24	0.56017		1729
Synonymous	-0.349	161	155	1.04	0.00000772	1533
Loss of Function	4.07	10	36.5	0.274	0.00000203	435

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Major helicase player in mitochondrial RNA metabolism. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. ATPase and ATP- dependent multisubstrate helicase, able to unwind double-stranded (ds) DNA and RNA, and RNA/DNA heteroduplexes in the 5'-to-3' direction. Plays a role in the RNA surveillance system in mitochondria; regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. Also implicated in recombination and chromatin maintenance pathways. May protect cells from apoptosis. Associates with mitochondrial DNA. {ECO:0000269|PubMed:12466530, ECO:0000269|PubMed:15096047, ECO:0000269|PubMed:17352692, ECO:0000269|PubMed:17961633, ECO:0000269|PubMed:18678873, ECO:0000269|PubMed:19509288, ECO:0000269|PubMed:19864255}.;

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.552
RVIS EVS: -0.98
RVIS percentile EVS: 8.85

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.943

Gene Damage Prediction

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