SUPV3L1

Suv3 like RNA helicase, the group of RNA helicases

Basic information

Region (hg38): 10:69180234-69209099

Links

ENSG00000156502 ∙ NCBI:6832 ∙ OMIM:605122 ∙ HGNC:11471 ∙ Uniprot:Q8IYB8 ∙ 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 SUPV3L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPV3L1 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				2		2
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	0

Variants in SUPV3L1

This is a list of pathogenic ClinVar variants found in the SUPV3L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-69180304-C-G		not specified	Uncertain significance (Feb 22, 2023)
10-69180307-G-T		not specified	Uncertain significance (Feb 13, 2024)
10-69180377-G-A		not specified	Uncertain significance (Oct 16, 2023)
10-69180390-G-A			Likely benign (Apr 01, 2022)
10-69180418-T-G		not specified	Uncertain significance (May 06, 2022)
10-69180452-G-C		not specified	Uncertain significance (Dec 17, 2023)
10-69180461-A-G		not specified	Uncertain significance (Nov 30, 2022)
10-69180488-C-T		not specified	Uncertain significance (Aug 17, 2021)
10-69180508-G-A		not specified	Uncertain significance (Aug 01, 2022)
10-69186479-A-C		not specified	Uncertain significance (Oct 04, 2022)
10-69186536-T-C		not specified	Uncertain significance (Dec 12, 2023)
10-69186544-G-A		not specified	Likely benign (Jan 23, 2024)
10-69187665-T-A		not specified	Uncertain significance (Feb 14, 2023)
10-69187689-A-G		not specified	Uncertain significance (Dec 06, 2022)
10-69187722-C-T		not specified	Uncertain significance (Sep 14, 2021)
10-69189356-A-T		not specified	Uncertain significance (Apr 20, 2024)
10-69189365-C-A		not specified	Uncertain significance (Jun 17, 2022)
10-69189427-A-G		not specified	Uncertain significance (Feb 11, 2022)
10-69191758-C-G		not specified	Uncertain significance (Aug 02, 2021)
10-69197036-A-G		not specified	Uncertain significance (Jan 30, 2024)
10-69197066-A-G		not specified	Uncertain significance (Dec 13, 2022)
10-69198382-A-G		not specified	Uncertain significance (Oct 26, 2022)
10-69198442-G-A		not specified	Uncertain significance (Apr 18, 2023)
10-69198495-C-T		not specified	Uncertain significance (Jul 14, 2021)
10-69199143-A-G		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUPV3L1	protein_coding	protein_coding	ENST00000359655	15	28868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0320	0.968	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	364	431	0.845	0.0000215	5157
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.000165	0.000163
South Asian	0.000235	0.000229
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.618
• ghis: 0.576

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Supv3l1
• Phenotype: skeleton phenotype; immune system phenotype; hearing/vestibular/ear phenotype; digestive/alimentary phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: supv3l1
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: mitochondrial mRNA catabolic process;positive regulation of mitochondrial RNA catabolic process;mitochondrial RNA 3'-end processing;DNA recombination;RNA catabolic process;positive regulation of cell growth;DNA duplex unwinding;mitochondrial ncRNA surveillance;mitochondrial mRNA surveillance;negative regulation of apoptotic process;mitochondrion morphogenesis;chromatin maintenance;mitochondrial RNA surveillance
• Cellular component: nucleus;mitochondrion;mitochondrial matrix;mitochondrial nucleoid;mitochondrial degradosome
• Molecular function: DNA binding;DNA helicase activity;RNA binding;double-stranded RNA binding;ATP-dependent RNA helicase activity;helicase activity;protein binding;ATP binding;3'-5' RNA helicase activity;protein homodimerization activity