SH3RF2

SH3 domain containing ring finger 2, the group of Protein phosphatase 1 regulatory subunits|Ring finger proteins

Basic information

Region (hg38): 5:145936578-146081791

Previous symbols: [ "PPP1R39" ]

Links

ENSG00000156463 ∙ NCBI:153769 ∙ OMIM:613377 ∙ HGNC:26299 ∙ Uniprot:Q8TEC5 ∙ 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 SH3RF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3RF2 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						0
missense			71	1		72
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	1	0

Variants in SH3RF2

This is a list of pathogenic ClinVar variants found in the SH3RF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-145937972-G-A		not specified	Uncertain significance (Jan 17, 2024)
5-145938070-C-T		not specified	Uncertain significance (May 27, 2022)
5-145938076-C-T		not specified	Uncertain significance (Jul 29, 2022)
5-145938107-T-C		not specified	Uncertain significance (Feb 02, 2024)
5-145938136-G-A		not specified	Uncertain significance (Nov 09, 2024)
5-145938171-C-G		not specified	Uncertain significance (Jan 17, 2024)
5-145938184-G-C		not specified	Uncertain significance (Oct 01, 2024)
5-145938208-A-G		not specified	Uncertain significance (Jul 16, 2024)
5-145938217-C-A		not specified	Uncertain significance (Feb 13, 2024)
5-145938229-A-G		not specified	Uncertain significance (Aug 05, 2024)
5-145938233-G-C		not specified	Uncertain significance (Jan 31, 2024)
5-145938242-A-C		not specified	Uncertain significance (May 31, 2023)
5-145938244-C-T		not specified	Uncertain significance (Nov 18, 2022)
5-145938271-C-T		not specified	Uncertain significance (May 29, 2024)
5-146000103-G-A		not specified	Uncertain significance (May 30, 2024)
5-146000160-AATTGGTACCAGGGGGAAATCAATGGCATCAGCGGGAACTTCCCAGCC-A			Uncertain significance (Jun 03, 2024)
5-146000169-CA-C			Uncertain significance (Apr 11, 2024)
5-146000250-C-T		not specified	Uncertain significance (Nov 26, 2024)
5-146000256-A-G		not specified	Uncertain significance (Sep 30, 2024)
5-146000274-G-A		not specified	Uncertain significance (Apr 19, 2024)
5-146000286-A-G		not specified	Uncertain significance (Mar 14, 2024)
5-146000289-G-A		not specified	Uncertain significance (Sep 17, 2021)
5-146000311-G-T		not specified	Uncertain significance (Nov 21, 2023)
5-146000317-C-T		not specified	Uncertain significance (Dec 06, 2021)
5-146004062-A-G		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3RF2	protein_coding	protein_coding	ENST00000511217	9	145213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-13	0.164	125614	0	134	125748	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.124	448	441	1.02	0.0000268	4704
Missense in Polyphen		145	135.89	1.067		1494
Synonymous	-0.997	209	191	1.09	0.0000124	1577
Loss of Function	0.941	23	28.4	0.810	0.00000163	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000994	0.000993
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000223	0.000217
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000653	0.000651
Middle Eastern	0.000223	0.000217
South Asian	0.000721	0.000719
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has E3 ubiquitin-protein ligase activity (PubMed:24130170). Acts as an anti-apoptotic regulator of the JNK pathway by ubiquitinating and promoting the degradation of SH3RF1, a scaffold protein that is required for pro-apoptotic JNK activation (PubMed:22128169). Facilitates TNF-alpha-mediated recruitment of adapter proteins TRADD and RIPK1 to TNFRSF1A and regulates PAK4 protein stability via inhibition of its ubiquitin- mediated proteasomal degradation (PubMed:24130170). Inhibits PPP1CA phosphatase activity (PubMed:19945436, PubMed:19389623). {ECO:0000269|PubMed:19389623, ECO:0000269|PubMed:19945436, ECO:0000269|PubMed:22128169, ECO:0000269|PubMed:24130170}.

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• loftool: 0.554
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.32

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.170
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3rf2

Gene ontology

• Biological process: negative regulation of phosphatase activity;positive regulation of cell migration;negative regulation of protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of phosphoprotein phosphatase activity;negative regulation of apoptotic process;negative regulation of JNK cascade;positive regulation of JNK cascade;protein autoubiquitination
• Cellular component: nucleus;nucleoplasm
• Molecular function: protein phosphatase inhibitor activity;protein binding;protein phosphatase 1 binding;phosphatase binding;metal ion binding;ubiquitin protein ligase activity