GeneBe

RNF113A

protein-coding

ring finger protein 113A, the group of Ring finger proteins|Spliceosomal C complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins

Gene summary

This intronless gene encodes a protein which contains a C3H1-type zinc finger domain and a C3HC4 Ring-type (Really Interesting New Gene-type) zinc finger domain. The Ring-type zinc finger domain is identified in various tumor suppressors, DNA repair genes and cytokine receptor-associated molecules, and is probably involved in mediating protein-protein interactions. [provided by RefSeq, May 2010]

Previous symbols:
  • ZNF183

MANE transcript

NM_006978.3

Inheritance

XL, AR

ClinVar variants

P:7U:93B:29

Top phenotype

Trichothiodystrophy 5, nonphotosensitive

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:119,870,475-119,871,733

External References & Databases

Ensembl (ENSG00000125352)NCBI Gene (7737)OMIM (300951)HGNC:12974GenCCUniProt (O15541)AlphaFoldClinVar (RNF113A)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~1.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

trichothiodystrophy 5, nonphotosensitiveSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: Labcorp Genetics (formerly Invitae)

trichothiodystrophy 5, nonphotosensitiveLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: Ambry Genetics

trichothiodystrophy 5, nonphotosensitiveLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: G2P

trichothiodystrophy 5, nonphotosensitiveLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: Genomics England PanelApp

trichothiodystrophy 5, nonphotosensitiveMODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: Illumina

trichothiodystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018053

Submitter: Orphanet

trichothiodystrophy 5, nonphotosensitiveSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010495

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Trichothiodystrophy 5, nonphotosensitiveXL

Manifestation: Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Endocrine; Genitourinary; Musculoskeletal; Neurologic

Intervention: Allergy/Immunology/Infectious

Rationale: The condition can involve recurrent infections, and awareness may allow preventive measures, and early and aggressive treatment of infections

Refs: 19377476; 25612912; 31130284; 31880405Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RNF113A variants in ClinVar

6 Conditions Cataloged
not providedTotal: 113
not specifiedTotal: 28
Trichothiodystrophy 5, nonphotosensitiveTotal: 10
RNF113A-related disorderTotal: 7
Abnormal cerebral morphologyTotal: 1
See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006978.3. 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.

EffectPLPVUSLBBSum
synonymous
16
clinvar
20
clinvar
1
clinvar
 37
missense
2
clinvar
76
clinvar
7
clinvar
1
clinvar
 86
nonsense
1
clinvar
1
clinvar
 2
start loss
0
frameshift
1
clinvar
2
clinvar
1
clinvar
 4
splice donor/acceptor (+/-2bp)
0
Total2593272129
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006978.3RefSeqNP_008909.11MANE Select
ENST00000371442.4EnsemblENSP00000360497.21MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
rnf113aDanio rerio

Structure: anatomical system

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • DNA repair
  • mRNA processing
  • protein ubiquitination
  • isopeptide cross-linking via N6-glycyl-L-lysine
  • snoRNA splicing

Molecular Function

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

Cellular Component

  • U2-type spliceosomal complex
  • nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000371442
Coding exons
1
Length
1295
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.77771350.5710.000008972285
Missense (PolyPhen)537.2960.13406631
Synonymous0.7214551.60.8720.00000350646
Loss of Function2.4707.130.004.58e-7132

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase that catalyzes the transfer of ubiquitin onto target proteins (PubMed:28978524, PubMed:29144457). Catalyzes polyubiquitination of SNRNP200/BRR2 with non-canonical 'Lys-63'-linked polyubiquitin chains (PubMed:29144457). Plays a role in DNA repair via its role in the synthesis of 'Lys-63'-linked polyubiquitin chains that recruit ALKBH3 and the ASCC complex to sites of DNA damage by alkylating agents (PubMed:29144457). Ubiquitinates CXCR4, leading to its degradation, and thereby contributes to the termination of CXCR4 signaling (PubMed:28978524). {ECO:0000269|PubMed:28978524, ECO:0000269|PubMed:29144457}.;

Recessive Scores

pRec
0.0928

Intolerance Scores

RVIS EVS
0.55
RVIS percentile EVS
81.22

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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