SH3RF3

SH3 domain containing ring finger 3, the group of Ring finger proteins

Basic information

Region (hg38): 2:109129205-109504634

Previous symbols: [ "SH3MD4" ]

Links

ENSG00000172985 ∙ NCBI:344558 ∙ OMIM:618933 ∙ HGNC:24699 ∙ Uniprot:Q8TEJ3 ∙ 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 SH3RF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3RF3 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
missense			55	6		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	7	0

Variants in SH3RF3

This is a list of pathogenic ClinVar variants found in the SH3RF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-109129610-G-A		not specified	Uncertain significance (Nov 04, 2022)
2-109129632-G-C		not specified	Uncertain significance (Feb 01, 2023)
2-109129638-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-109129641-G-A		not specified	Uncertain significance (May 08, 2024)
2-109129650-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-109129714-C-T			Likely benign (Sep 01, 2022)
2-109129771-C-G		not specified	Uncertain significance (Dec 16, 2023)
2-109129799-T-A		not specified	Uncertain significance (Mar 30, 2024)
2-109129810-C-G		not specified	Uncertain significance (Jan 30, 2024)
2-109129929-G-T		not specified	Uncertain significance (Dec 06, 2023)
2-109129947-C-G		not specified	Uncertain significance (Jun 07, 2023)
2-109129958-A-G		not specified	Likely benign (May 30, 2024)
2-109129974-C-T		not specified	Uncertain significance (May 13, 2022)
2-109129982-A-C		not specified	Uncertain significance (Sep 16, 2021)
2-109129988-G-A		not specified	Uncertain significance (May 25, 2022)
2-109130030-C-A		not specified	Uncertain significance (Aug 02, 2022)
2-109130043-C-T		not specified	Uncertain significance (Dec 28, 2023)
2-109130063-G-A		not specified	Likely benign (Sep 07, 2022)
2-109130070-G-A		not specified	Uncertain significance (Dec 06, 2021)
2-109130073-T-C		not specified	Uncertain significance (Sep 07, 2022)
2-109130075-C-T		not specified	Uncertain significance (Dec 21, 2023)
2-109130084-G-T		not specified	Uncertain significance (Dec 21, 2023)
2-109347758-A-G		not specified	Likely benign (Nov 08, 2022)
2-109347771-G-A		not specified	Uncertain significance (Jun 16, 2023)
2-109347809-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3RF3	protein_coding	protein_coding	ENST00000309415	10	516404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0284	0.972	125066	0	18	125084	0.0000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	394	489	0.805	0.0000307	5539
Missense in Polyphen		102	173.61	0.58752		1923
Synonymous	-1.21	247	224	1.10	0.0000156	1939
Loss of Function	3.43	8	27.4	0.292	0.00000126	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000150
Ashkenazi Jewish	0.000104	0.0000993
East Asian	0.00	0.00
Finnish	0.000144	0.000139
European (Non-Finnish)	0.0000534	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.000136	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has E3 ubiquitin-protein ligase activity. {ECO:0000269|PubMed:20696164}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.484
• ghis: 0.475

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0461

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3rf3

Gene ontology

• Biological process: positive regulation of JNK cascade;protein autoubiquitination
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity