RNF10

ring finger protein 10, the group of Ring finger proteins

Basic information

Region (hg38): 12:120533480-120577588

Links

ENSG00000022840 ∙ NCBI:9921 ∙ OMIM:615998 ∙ HGNC:10055 ∙ Uniprot:Q8N5U6 ∙ 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 RNF10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF10 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				1		1
missense			58	2	1	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	1

Variants in RNF10

This is a list of pathogenic ClinVar variants found in the RNF10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-120534842-A-G		not specified	Uncertain significance (Mar 07, 2024)
12-120534864-A-G		not specified	Uncertain significance (Dec 22, 2023)
12-120534868-C-A		not specified	Uncertain significance (Nov 23, 2022)
12-120534870-G-C		not specified	Uncertain significance (Apr 15, 2024)
12-120534876-A-G		not specified	Likely benign (Apr 07, 2023)
12-120534893-T-A		not specified	Uncertain significance (Jun 29, 2023)
12-120534953-T-C		not specified	Uncertain significance (Dec 16, 2024)
12-120534953-T-G		not specified	Uncertain significance (Sep 11, 2024)
12-120546414-A-G		not specified	Uncertain significance (Jan 28, 2025)
12-120546431-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-120546432-G-A		not specified	Uncertain significance (Oct 18, 2021)
12-120546441-G-A		not specified	Uncertain significance (Jun 02, 2023)
12-120546441-G-T		not specified	Uncertain significance (Dec 09, 2024)
12-120546449-G-C		not specified	Uncertain significance (Dec 31, 2024)
12-120546464-A-C		not specified	Uncertain significance (Dec 10, 2024)
12-120546468-A-G		not specified	Uncertain significance (Dec 11, 2023)
12-120546491-C-T		not specified	Uncertain significance (Jul 30, 2024)
12-120546494-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-120546534-C-T		not specified	Uncertain significance (Sep 23, 2023)
12-120546539-C-G		not specified	Uncertain significance (Nov 09, 2023)
12-120546551-G-A		not specified	Uncertain significance (Jul 13, 2021)
12-120546580-T-C			Likely benign (Jul 16, 2018)
12-120552532-G-A		not specified	Uncertain significance (Oct 24, 2023)
12-120552557-T-A		not specified	Uncertain significance (Jun 16, 2023)
12-120552605-C-T		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF10	protein_coding	protein_coding	ENST00000325954	17	44115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.836	125596	0	152	125748	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.777	416	463	0.898	0.0000255	5326
Missense in Polyphen		78	121.7	0.64095		1354
Synonymous	0.470	163	171	0.954	0.00000906	1573
Loss of Function	4.51	10	41.3	0.242	0.00000200	495

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000632	0.000570
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.000253	0.000231
European (Non-Finnish)	0.00114	0.00113
Middle Eastern	0.000168	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor involved in the regulation of MAG (Myelin-associated glycoprotein) expression. Acts as a regulator of Schwann cell differentiation and myelination. {ECO:0000250|UniProtKB:Q5XI59}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.150
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.309
• hipred: N
• hipred_score: 0.426
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf10
• Phenotype: immune system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye 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); 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); homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of Schwann cell proliferation;positive regulation of myelination;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein autoubiquitination
• Cellular component: nucleus;cytoplasm
• Molecular function: ubiquitin-protein transferase activity;protein binding;transcription regulatory region DNA binding;metal ion binding