RNF128

ring finger protein 128, the group of Ring finger proteins

Basic information

Region (hg38): X:106693794-106797016

Links

ENSG00000133135 ∙ NCBI:79589 ∙ OMIM:300439 ∙ HGNC:21153 ∙ Uniprot:Q8TEB7 ∙ 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 RNF128 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF128 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	2
missense			25	3	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	25	5	2

Variants in RNF128

This is a list of pathogenic ClinVar variants found in the RNF128 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-106693986-A-C		RNF128-related disorder	Likely benign (Feb 22, 2022)
X-106694345-G-A			Likely benign (-)
X-106726930-G-C		not specified	Uncertain significance (Dec 31, 2023)
X-106726933-C-A		not specified	Uncertain significance (Aug 22, 2023)
X-106726936-G-A		not specified	Uncertain significance (Jan 23, 2023)
X-106726977-G-A		not specified	Uncertain significance (Jan 13, 2023)
X-106727067-C-T		not specified	Uncertain significance (Jan 02, 2024)
X-106727195-C-T			Benign (Apr 03, 2018)
X-106727205-C-A		not specified	Uncertain significance (Feb 27, 2023)
X-106727215-A-T		not specified	Uncertain significance (May 29, 2024)
X-106727295-T-G			Uncertain significance (Sep 01, 2019)
X-106727324-G-C		not specified	Uncertain significance (Dec 27, 2022)
X-106727370-A-G		not specified	Uncertain significance (May 23, 2023)
X-106727394-C-T		not specified	Uncertain significance (Dec 21, 2023)
X-106772930-G-A		not specified	Uncertain significance (Dec 09, 2023)
X-106772941-C-T			Likely benign (Sep 01, 2022)
X-106772942-G-A		Laterality defects, autosomal dominant	Uncertain significance (-)
X-106772942-G-T		not specified	Uncertain significance (Nov 30, 2022)
X-106773038-A-T			Benign (Dec 31, 2019)
X-106773040-T-A		not specified	Uncertain significance (Jul 19, 2023)
X-106773051-T-C		not specified	Uncertain significance (Jan 09, 2024)
X-106773059-G-A			Likely benign (May 16, 2018)
X-106773084-C-T		not specified	Uncertain significance (Dec 03, 2021)
X-106785126-A-G		not specified	Uncertain significance (Apr 12, 2024)
X-106787984-C-T		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF128	protein_coding	protein_coding	ENST00000255499	7	103200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.228	0.765	125737	3	4	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.666	141	165	0.854	0.0000120	2752
Missense in Polyphen		47	64.071	0.73356		1027
Synonymous	0.707	61	68.4	0.891	0.00000512	891
Loss of Function	2.33	3	11.5	0.260	7.86e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000825	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000145	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000368	0.0000264
Middle Eastern	0.000145	0.000109
South Asian	0.0000534	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that catalyzes 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains formation. Functions as an inhibitor of cytokine gene transcription. Inhibits IL2 and IL4 transcription, thereby playing an important role in the induction of the anergic phenotype, a long-term stable state of T-lymphocyte unresponsiveness to antigenic stimulation associated with the blockade of interleukin production. Ubiquitinates ARPC5 with 'Lys- 48' linkages and COR1A with 'Lys-63' linkages leading to their degradation, down-regulation of these cytosleletal components results in impaired lamellipodium formation and reduced accumulation of F-actin at the immunological synapse. Functions in the patterning of the dorsal ectoderm; sensitizes ectoderm to respond to neural-inducing signals. {ECO:0000269|PubMed:12705856, ECO:0000269|PubMed:22016387}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Ovarian tumor domain proteases;Deubiquitination;Calcineurin-regulated NFAT-dependent transcription in lymphocytes (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.651
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.598
• hipred: Y
• hipred_score: 0.845
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.566

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf128
• Phenotype: respiratory system phenotype; hematopoietic system 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); cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;protein deubiquitination;regulation of protein stability;negative regulation of cytokine biosynthetic process;protein localization to lysosome;positive regulation of protein catabolic process in the vacuole
• Cellular component: late endosome;endoplasmic reticulum;Golgi apparatus;cytosol;cytoskeleton;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity