RNF10

protein-coding

ring finger protein 10, the group of Ring finger proteins

Gene summary

The protein encoded by this gene contains a ring finger motif, which is known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. EST data suggests the existence of multiple alternatively spliced transcript variants, however, their full length nature is not known. [provided by RefSeq, Jul 2008]

MANE transcript

NM_014868.5

Inheritance

—

ClinVar variants

U:119B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr12:120,533,480-120,577,588

External References & Databases

Ensembl (ENSG00000022840)

Transcript & Mutation Effects

hg38 • Region Span ~44.1 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 RNF10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014868.5. 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			2 clinvar	1 clinvar		3
missense			109 clinvar	4 clinvar	1 clinvar	114
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	119	5	1	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014868.5	RefSeq	NP_055683.3	17	MANE Select
ENST00000325954.9	Ensembl	ENSP00000322242.4	17	MANE Select
NM_001330474.2	RefSeq	NP_001317403.1	17	Standard
ENST00000413266.6	Ensembl	ENSP00000415682.2	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

ubiquitin-protein transferase activity
protein binding
transcription regulatory region DNA binding
metal ion binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325954
Coding exons: 17
Length: 44115
Individuals with no LoFs: 125596
Homozygous LoFs: 0
Heterozygous LoFs: 152
Defined: 125748
p: 0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.777	416	463	0.898	0.0000255	5326
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00031	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0.00025	0.00023	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.963

Gene Damage Prediction

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