SH3RF1
Basic information
Region (hg38): 4:169094259-169270956
Previous symbols: [ "SH3MD2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (89 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3RF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020870.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 85 | 90 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 85 | 4 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SH3RF1 | protein_coding | protein_coding | ENST00000284637 | 11 | 176850 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0108 | 0.989 | 125735 | 0 | 13 | 125748 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.51 | 417 | 513 | 0.812 | 0.0000284 | 5700 |
Missense in Polyphen | 140 | 217.15 | 0.64471 | 2478 | ||
Synonymous | 1.30 | 183 | 207 | 0.885 | 0.0000124 | 1930 |
Loss of Function | 3.77 | 10 | 33.6 | 0.298 | 0.00000189 | 381 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000620 | 0.0000615 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000926 | 0.0000924 |
European (Non-Finnish) | 0.0000716 | 0.0000703 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has E3 ubiquitin-protein ligase activity. In the absence of an external substrate, it can catalyze self-ubiquitination (PubMed:15659549, PubMed:20696164). Stimulates ubiquitination of potassium channel KCNJ1, enhancing it's dynamin-dependent and clathrin-independent endocytosis (PubMed:19710010). Acts as a scaffold protein that coordinates with MAPK8IP1/JIP1 in organizing different components of the JNK pathway, including RAC1 or RAC2, MAP3K11/MLK3 or MAP3K7/TAK1, MAP2K7/MKK7, MAPK8/JNK1 and/or MAPK9/JNK2 into a functional multiprotein complex to ensure the effective activation of the JNK signaling pathway. Regulates the differentiation of CD4(+) and CD8(+) T-cells and promotes T-helper 1 (Th1) cell differentiation. Regulates the activation of MAPK8/JNK1 and MAPK9/JNK2 in CD4(+) T-cells and the activation of MAPK8/JNK1 in CD8(+) T-cells. Plays a crucial role in the migration of neocortical neurons in the developing brain. Controls proper cortical neuronal migration and the formation of proximal cytoplasmic dilation in the leading process (PCDLP) in migratory neocortical neurons by regulating the proper localization of activated RAC1 and F-actin assembly (By similarity). {ECO:0000250|UniProtKB:Q69ZI1, ECO:0000269|PubMed:15659549, ECO:0000269|PubMed:19710010, ECO:0000269|PubMed:20696164}.;
- Pathway
- EGF-Ncore;G13 Signaling Pathway;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.138
Intolerance Scores
- loftool
- 0.303
- rvis_EVS
- -0.57
- rvis_percentile_EVS
- 18.96
Haploinsufficiency Scores
- pHI
- 0.666
- hipred
- Y
- hipred_score
- 0.670
- ghis
- 0.538
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.896
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sh3rf1
- Phenotype
Gene ontology
- Biological process
- neuron migration;apoptotic process;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of CD4-positive, alpha-beta T cell differentiation;positive regulation of JNK cascade;protein autoubiquitination;regulation of CD8-positive, alpha-beta T cell proliferation;negative regulation of extrinsic apoptotic signaling pathway
- Cellular component
- Golgi apparatus;cytosol;lamellipodium;perinuclear region of cytoplasm
- Molecular function
- MAP-kinase scaffold activity;protein binding;metal ion binding;ubiquitin protein ligase activity