RNF170

ring finger protein 170, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 8:42849636-42897290

Previous symbols: [ "SNAX1" ]

Links

ENSG00000120925 ∙ NCBI:81790 ∙ OMIM:614649 ∙ HGNC:25358 ∙ Uniprot:Q96K19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant sensory ataxia 1 (Strong), mode of inheritance: AD
• spastic paraplegia 85, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ataxia, sensory, 1, autosomal dominant; Spastic paraplegia 85, autosomal recessive	AD/AR	General	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	Neurologic; Ophthalmologic	17190954; 21115467; 31636353

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF170 gene.

• not provided (10 variants)
• Autosomal dominant sensory ataxia 1 (8 variants)
• Spastic paraplegia 85, autosomal recessive (6 variants)
• Inborn genetic diseases (4 variants)
• not specified (2 variants)
• Spastic paraplegia (2 variants)
• RNF170-related condition (1 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF170 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	1	1	9	2		13
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	1			2
non coding					2	2
Total	2	1	9	3	3

Highest pathogenic variant AF is 0.00000658

Variants in RNF170

This is a list of pathogenic ClinVar variants found in the RNF170 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42850871-C-T		not specified	Benign (-)
8-42850874-G-A		Autosomal dominant sensory ataxia 1	Uncertain significance (Jun 19, 2020)
8-42850904-C-T		Autosomal dominant sensory ataxia 1	Uncertain significance (May 13, 2016)
8-42850975-C-T		Inborn genetic diseases	Uncertain significance (Sep 15, 2021)
8-42856296-T-C		Autosomal dominant sensory ataxia 1 • not specified	Conflicting classifications of pathogenicity (Jan 24, 2023)
8-42856341-G-A		Autosomal dominant sensory ataxia 1 • Spastic paraplegia 85, autosomal recessive	Pathogenic (Mar 20, 2023)
8-42856362-C-T			Uncertain significance (Jan 01, 2024)
8-42856370-A-C		Autosomal dominant sensory ataxia 1	Conflicting classifications of pathogenicity (Jul 12, 2021)
8-42856416-TTC-T		Spastic paraplegia 85, autosomal recessive	Pathogenic (Jan 05, 2022)
8-42856463-A-G			Benign (May 15, 2021)
8-42861759-C-G		Autosomal dominant sensory ataxia 1	Uncertain significance (Feb 14, 2023)
8-42861868-G-GA			Likely benign (-)
8-42865413-T-C		Spastic paraplegia • Spastic paraplegia 85, autosomal recessive	Likely pathogenic (Jun 17, 2021)
8-42865416-C-T		Spastic paraplegia 85, autosomal recessive	Uncertain significance (Mar 22, 2022)
8-42865438-C-T		Autosomal dominant sensory ataxia 1 • not specified	Benign/Likely benign (Apr 01, 2023)
8-42865461-A-G			Likely benign (Oct 01, 2023)
8-42865465-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
8-42865466-G-A		Autosomal dominant sensory ataxia 1 • Spastic paraplegia 85, autosomal recessive	Conflicting classifications of pathogenicity (Mar 22, 2022)
8-42865470-G-C		Neurodevelopmental disorder	Pathogenic (Jun 17, 2021)
8-42869991-G-A			Benign (May 22, 2021)
8-42870005-A-C		Spastic paraplegia 85, autosomal recessive	Likely pathogenic (Jun 10, 2022)
8-42870022-A-G		Autosomal dominant sensory ataxia 1 • Spastic paraplegia 85, autosomal recessive • Spastic paraplegia	Conflicting classifications of pathogenicity (Mar 22, 2022)
8-42870035-C-T			Benign (Dec 31, 2019)
8-42870036-G-A			Uncertain significance (Feb 01, 2024)
8-42870042-G-A			Uncertain significance (Apr 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF170	protein_coding	protein_coding	ENST00000534961	6	47654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.511	0.488	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	93	140	0.663	0.00000701	1686
Missense in Polyphen		20	37.733	0.53004		477
Synonymous	0.810	40	47.1	0.850	0.00000224	496
Loss of Function	2.86	3	14.9	0.201	8.48e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000911
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000555	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that plays an essential role in stimulus-induced inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) ubiquitination and degradation via the endoplasmic reticulum-associated degradation (ERAD) pathway. Also involved in ITPR1 turnover in resting cells. {ECO:0000269|PubMed:21610068}.

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• loftool: 0.174
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.595
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf170
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: rnf170
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity