RNF13

protein-coding

ring finger protein 13, the group of Ring finger proteins

Gene summary

The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. The specific function of this gene has not yet been determined. Alternatively spliced transcript variants that encode the same protein have been reported. A pseudogene, which is also located on chromosome 3, has been defined for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_183381.3

Inheritance

ClinVar variants

P:9U:147B:104

Top phenotype

Developmental and epileptic encephalopathy 73

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr3:149,812,770-149,962,139

External References & Databases

Ensembl (ENSG00000082996)

Transcript & Mutation Effects

hg38 • Region Span ~149.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

developmental and epileptic encephalopathy, 73STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0034106

Submitter: PanelApp Australia

developmental and epileptic encephalopathy, 73LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0034106

Submitter: Ambry Genetics

developmental and epileptic encephalopathy, 73STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0034106

Submitter: Labcorp Genetics (formerly Invitae)

developmental and epileptic encephalopathy, 73STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0034106

Submitter: G2P

Clinical Genomic Database (CGD)

Developmental and epileptic encephalopathy 73AD

Manifestation: Audiologic/Otolaryngologic; Craniofacial; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 30595371

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RNF13 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 271

not specifiedTotal: 45

Developmental and epileptic encephalopathy, 73Total: 19

RNF13-related disorderTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_183381.3. 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				63 clinvar		63
missense	2 clinvar		127 clinvar	27 clinvar	13 clinvar	169
nonsense	1 clinvar	3 clinvar	3 clinvar			7
start loss						0
frameshift		3 clinvar	9 clinvar			12
splice donor/acceptor (+/-2bp)			8 clinvar		1 clinvar	9
Total	3	6	147	90	14	260

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 150 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_183381.3	RefSeq	NP_899237.1	9	MANE Select
ENST00000392894.8	Ensembl	ENSP00000376628.3	9	MANE Select
NM_001378285.1	RefSeq	NP_001365214.1	9	Standard
NM_001378286.1	RefSeq	NP_001365215.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ubiquitin-dependent protein catabolic process
protein autoubiquitination

Molecular Function

ubiquitin-protein transferase activity
protein binding
metal ion binding
ubiquitin protein ligase activity

Cellular Component

Golgi membrane
nuclear inner membrane
nucleoplasm
lysosomal membrane
endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344229
Coding exons: 9
Length: 149432
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125744
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.901	158	193	0.818	0.00000919	2506
Missense (PolyPhen)		39	57.7	0.67591		788
Synonymous	-0.618	77	70.4	1.09	0.00000353	705
Loss of Function	1.86	8	16.0	0.499	6.69e-7	244

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation. {ECO:0000269|PubMed:18794910}.;

Recessive Scores

pRec: 0.0875

Intolerance Scores

LoFtool: 0.732
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.866

Gene Damage Prediction

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