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GeneBe

RNF10

ring finger protein 10, the group of Ring finger proteins

Basic information

Region (hg38): 12:120533479-120577588

Links

ENSG00000022840NCBI:9921OMIM:615998HGNC:10055Uniprot:Q8N5U6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF10 gene.

  • Inborn genetic diseases (28 variants)
  • not provided (2 variants)

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
clinvar
1
missense
27
clinvar
1
clinvar
1
clinvar
29
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 27 2 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)3154906
12-120534864-A-G not specified Uncertain significance (Dec 22, 2023)3154908
12-120534868-C-A not specified Uncertain significance (Nov 23, 2022)2329502
12-120534876-A-G not specified Likely benign (Apr 07, 2023)2534525
12-120534893-T-A not specified Uncertain significance (Jun 29, 2023)2608853
12-120534953-T-G not specified Uncertain significance (Jan 10, 2022)2217483
12-120546432-G-A not specified Uncertain significance (Oct 18, 2021)2255720
12-120546441-G-A not specified Uncertain significance (Jun 02, 2023)2546220
12-120546468-A-G not specified Uncertain significance (Dec 11, 2023)3154903
12-120546494-C-T not specified Uncertain significance (Dec 19, 2022)2337565
12-120546534-C-T not specified Uncertain significance (Sep 23, 2023)3154904
12-120546539-C-G not specified Uncertain significance (Nov 09, 2023)3154905
12-120546551-G-A not specified Uncertain significance (Jul 13, 2021)2245346
12-120546580-T-C Likely benign (Jul 16, 2018)727629
12-120552532-G-A not specified Uncertain significance (Oct 24, 2023)3154907
12-120552557-T-A not specified Uncertain significance (Jun 16, 2023)2597659
12-120552605-C-T not specified Uncertain significance (Jun 21, 2023)2592272
12-120554723-A-G not specified Uncertain significance (Nov 27, 2023)3154909
12-120557315-A-G not specified Uncertain significance (May 23, 2023)2527848
12-120557328-C-T not specified Uncertain significance (Jan 03, 2024)3154910
12-120557565-C-T not specified Uncertain significance (Nov 09, 2021)2381654
12-120557593-C-T not specified Uncertain significance (Jan 26, 2023)2479365
12-120557599-A-G not specified Uncertain significance (Jan 03, 2024)3154911
12-120557619-G-A not specified Uncertain significance (May 09, 2022)2287992
12-120560776-G-T not specified Uncertain significance (Nov 22, 2023)3154894

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF10protein_codingprotein_codingENST00000325954 1744115
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1640.83612559601521257480.000605
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7774164630.8980.00002555326
Missense in Polyphen78121.70.640951354
Synonymous0.4701631710.9540.000009061573
Loss of Function4.511041.30.2420.00000200495

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006320.000570
Ashkenazi Jewish0.000.00
East Asian0.0001680.000163
Finnish0.0002530.000231
European (Non-Finnish)0.001140.00113
Middle Eastern0.0001680.000163
South Asian0.00006540.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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