RNF170 ring finger protein 170 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF170provided by HGNC
Official Full Name: ring finger protein 170provided by HGNC
Primary source: HGNC:HGNC:25358
See related: Ensembl:ENSG00000120925 MIM:614649; AllianceGenome:HGNC:25358
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ADSA; SNAX1; SPG85
Summary: This gene encodes a RING domain-containing protein that resides in the endoplasmic reticulum (ER) membrane. This protein functions as an E3 ubiquitin ligase and mediates ubiquitination and processing of inositol 1,4,5-trisphosphate (IP3) receptors via the ER-associated protein degradation pathway. It is recruited to the activated IP3 receptors by the ERLIN1/ERLIN2 complex to which it is constitutively bound. Mutations in this gene are associated with autosomal dominant sensory ataxia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]
Expression: Ubiquitous expression in thyroid (RPKM 10.8), brain (RPKM 6.2) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8p11.21

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (42849637..42897299, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (43117750..43166240, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (42704780..42751748, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNF170 mutation causes autosomal dominant sensory ataxia with variable pyramidal involvement.
Title: RNF170 mutation causes autosomal dominant sensory ataxia with variable pyramidal involvement.
RNF170-Related Hereditary Spastic Paraplegia: Confirmation by a Novel Mutation.
Title: RNF170-Related Hereditary Spastic Paraplegia: Confirmation by a Novel Mutation.
mutations in the ubiquitin E3 ligase gene RNF170, which targets inositol 1,4,5-trisphosphate receptors for degradation, are the likely cause of autosomal recessive HSP in four unrelated families and functionally evaluate the consequences of mutations in patient fibroblasts and mutant SH-SY5Y cells. Our findings highlight inositol 1,4,5-trisphosphate signaling as a candidate key pathway for hereditary spastic paraplegias.
Title: Bi-allelic variants in RNF170 are associated with hereditary spastic paraplegia.
aberrant ubiquitination of substrates, or cellular adaptation to chronically reduced RNF170 levels likely accounts for the autosomal dominant sensory ataxia-associated Ca2+ signaling deficit
Title: A Point Mutation in the Ubiquitin Ligase RNF170 That Causes Autosomal Dominant Sensory Ataxia Destabilizes the Protein and Impairs Inositol 1,4,5-Trisphosphate Receptor-mediated Ca2+ Signaling.
RNF170 plays an essential role in IP(3) receptor processing via the ubiquitin-proteasome pathway.
Title: RNF170 protein, an endoplasmic reticulum membrane ubiquitin ligase, mediates inositol 1,4,5-trisphosphate receptor ubiquitination and degradation.
Together these results suggest that the mutation in RNF170 is causal for the sensory ataxia
Title: A mutation in the RNF170 gene causes autosomal dominant sensory ataxia.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal dominant sensory ataxia 1 MedGen: C1837015 OMIM: 608984 GeneReviews: Not available	Compare labs
Spastic paraplegia 85, autosomal recessive MedGen: C5562053 OMIM: 619686 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of ring finger protein 170 (RNF170) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

D8S2279 (e-PCR)
- UniSTS:473907

D8S1555 (e-PCR)
- UniSTS:153656

SHGC-5737 (e-PCR)
- UniSTS:70260

D8S2120 (e-PCR)
- UniSTS:7093

D8S1340E (e-PCR)
- UniSTS:473309

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of toll-like receptor 3 signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF170

Names: RING-type E3 ubiquitin transferase RNF170; putative LAG1-interacting protein

NP_001153695.1

EC 2.3.2.27

NP_001153696.1

EC 2.3.2.27

NP_001153697.1

EC 2.3.2.27

NP_112216.3

EC 2.3.2.27

XP_006716467.1

EC 2.3.2.27

XP_006716468.1

EC 2.3.2.27

XP_011542968.1

EC 2.3.2.27

XP_016869370.1

EC 2.3.2.27

XP_047278234.1

EC 2.3.2.27

XP_047278235.1

EC 2.3.2.27

XP_047278236.1

EC 2.3.2.27

XP_047278237.1

EC 2.3.2.27

XP_047278238.1

EC 2.3.2.27

XP_047278239.1

EC 2.3.2.27

XP_047278240.1

EC 2.3.2.27

XP_047278241.1

EC 2.3.2.27

XP_047278242.1

EC 2.3.2.27

XP_047278243.1

EC 2.3.2.27

XP_047278244.1

EC 2.3.2.27

XP_054217281.1

EC 2.3.2.27

XP_054217282.1

EC 2.3.2.27

XP_054217283.1

EC 2.3.2.27

XP_054217284.1

EC 2.3.2.27

XP_054217285.1

EC 2.3.2.27

XP_054217286.1

EC 2.3.2.27

XP_054217287.1

EC 2.3.2.27

XP_054217288.1

EC 2.3.2.27

XP_054217289.1

EC 2.3.2.27

XP_054217290.1

EC 2.3.2.27

XP_054217291.1

EC 2.3.2.27

XP_054217292.1

EC 2.3.2.27

XP_054217293.1

EC 2.3.2.27

XP_054217294.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_032868.1 RefSeqGene

Range

5119..48423

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001160223.2 → NP_001153695.1 E3 ubiquitin-protein ligase RNF170 isoform a

See identical proteins and their annotated locations for NP_001153695.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AA973979, AC087533, BC039461, BG910500

Consensus CDS

CCDS6138.1

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6

Related

ENSP00000445725.1, ENST00000534961.5

Conserved Domains (2) summary

cd00162
Location:87 → 133

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam06803
Location:203 → 239

DUF1232; Protein of unknown function (DUF1232)
NM_001160224.2 → NP_001153696.1 E3 ubiquitin-protein ligase RNF170 isoform b

See identical proteins and their annotated locations for NP_001153696.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' and 3' UTRs and has multiple coding region differences compared to variant 1. This results in a shorter isoform (b) with a distinct C-terminus, compared to isoform a.

Source sequence(s)

AC087533, BC032393, DA751961

Consensus CDS

CCDS55230.1

UniProtKB/Swiss-Prot

Q96K19

Related

ENSP00000326138.3, ENST00000319104.7

Conserved Domains (1) summary

cd00162
Location:87 → 132

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
NM_001160225.2 → NP_001153697.1 E3 ubiquitin-protein ligase RNF170 isoform c

See identical proteins and their annotated locations for NP_001153697.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (c) has a shorter N-terminus compared to isoform a.

Source sequence(s)

AA973979, AC087533, BC058289

Consensus CDS

CCDS55229.1

UniProtKB/Swiss-Prot

Q96K19

Related

ENSP00000435782.1, ENST00000526349.5

Conserved Domains (2) summary

pfam06803
Location:119 → 153

DUF1232; Protein of unknown function (DUF1232)

cd16553
Location:3 → 46

RING-HC_RNF170; RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins
NM_030954.4 → NP_112216.3 E3 ubiquitin-protein ligase RNF170 isoform a

See identical proteins and their annotated locations for NP_112216.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AA973979, AC087533, AK225568

Consensus CDS

CCDS6138.1

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6

Related

ENSP00000434797.1, ENST00000527424.6

Conserved Domains (2) summary

cd00162
Location:87 → 133

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam06803
Location:203 → 239

DUF1232; Protein of unknown function (DUF1232)

RNA

NR_027668.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA973979, AC087533, AK090864
NR_027669.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate 5' exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA973979, AC087533, BC013422, DA751961

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

42849637..42897299 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422281.1 → XP_047278237.1 E3 ubiquitin-protein ligase RNF170 isoform X4
XM_011544666.4 → XP_011542968.1 E3 ubiquitin-protein ligase RNF170 isoform X2

See identical proteins and their annotated locations for XP_011542968.1

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6

Conserved Domains (2) summary

cd00162
Location:87 → 133

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam06803
Location:203 → 239

DUF1232; Protein of unknown function (DUF1232)
XM_047422279.1 → XP_047278235.1 E3 ubiquitin-protein ligase RNF170 isoform X2

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6
XM_006716405.4 → XP_006716468.1 E3 ubiquitin-protein ligase RNF170 isoform X4

Conserved Domains (1) summary

pfam06803
Location:153 → 189

DUF1232; Protein of unknown function (DUF1232)
XM_006716404.3 → XP_006716467.1 E3 ubiquitin-protein ligase RNF170 isoform X2

See identical proteins and their annotated locations for XP_006716467.1

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6

Conserved Domains (2) summary

cd00162
Location:87 → 133

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam06803
Location:203 → 239

DUF1232; Protein of unknown function (DUF1232)
XM_017013881.2 → XP_016869370.1 E3 ubiquitin-protein ligase RNF170 isoform X2

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6

Conserved Domains (2) summary

cd00162
Location:87 → 133

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam06803
Location:203 → 239

DUF1232; Protein of unknown function (DUF1232)
XM_047422280.1 → XP_047278236.1 E3 ubiquitin-protein ligase RNF170 isoform X3
XM_047422278.1 → XP_047278234.1 E3 ubiquitin-protein ligase RNF170 isoform X1
XM_047422282.1 → XP_047278238.1 E3 ubiquitin-protein ligase RNF170 isoform X5
XM_047422285.1 → XP_047278241.1 E3 ubiquitin-protein ligase RNF170 isoform X8

Related

ENSP00000325969.5, ENST00000319073.5
XM_047422288.1 → XP_047278244.1 E3 ubiquitin-protein ligase RNF170 isoform X11
XM_047422287.1 → XP_047278243.1 E3 ubiquitin-protein ligase RNF170 isoform X10
XM_047422284.1 → XP_047278240.1 E3 ubiquitin-protein ligase RNF170 isoform X7

Related

ENSP00000436416.1, ENST00000531440.5
XM_047422283.1 → XP_047278239.1 E3 ubiquitin-protein ligase RNF170 isoform X6
XM_047422286.1 → XP_047278242.1 E3 ubiquitin-protein ligase RNF170 isoform X9

Alternate T2T-CHM13v2.0

Genomic

NC_060932.1 Alternate T2T-CHM13v2.0

Range

43117750..43166240 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054361308.1 → XP_054217283.1 E3 ubiquitin-protein ligase RNF170 isoform X2

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6
XM_054361312.1 → XP_054217287.1 E3 ubiquitin-protein ligase RNF170 isoform X4
XM_054361311.1 → XP_054217286.1 E3 ubiquitin-protein ligase RNF170 isoform X4
XM_054361307.1 → XP_054217282.1 E3 ubiquitin-protein ligase RNF170 isoform X2

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6
XM_054361309.1 → XP_054217284.1 E3 ubiquitin-protein ligase RNF170 isoform X2

UniProtKB/Swiss-Prot

D3DSY6, E9PIL4, Q7Z483, Q86YC0, Q8IXR7, Q8N2B5, Q8N5G9, Q8NG30, Q96K19, Q9H0V6
XM_054361310.1 → XP_054217285.1 E3 ubiquitin-protein ligase RNF170 isoform X3
XM_054361306.1 → XP_054217281.1 E3 ubiquitin-protein ligase RNF170 isoform X1
XM_054361313.1 → XP_054217288.1 E3 ubiquitin-protein ligase RNF170 isoform X5
XM_054361316.1 → XP_054217291.1 E3 ubiquitin-protein ligase RNF170 isoform X8
XM_054361319.1 → XP_054217294.1 E3 ubiquitin-protein ligase RNF170 isoform X11
XM_054361318.1 → XP_054217293.1 E3 ubiquitin-protein ligase RNF170 isoform X10
XM_054361315.1 → XP_054217290.1 E3 ubiquitin-protein ligase RNF170 isoform X7
XM_054361314.1 → XP_054217289.1 E3 ubiquitin-protein ligase RNF170 isoform X6
XM_054361317.1 → XP_054217292.1 E3 ubiquitin-protein ligase RNF170 isoform X9