SNF8
Basic information
Region (hg38): 17:48929316-48944842
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Developmental and epileptic encephalopathy 115; Neurodevelopmental disorder plus optic atrophy | 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 | 38423010 |
ClinVar
This is a list of variants' phenotypes submitted to
- SNF8-associated disease (6 variants)
- Developmental and epileptic encephalopathy 115 (4 variants)
- Neurodevelopmental disorder plus optic atrophy (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNF8 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 | 10 | 13 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 6 | 0 | 10 | 0 | 0 |
Highest pathogenic variant AF is 0.00000658
Variants in SNF8
This is a list of pathogenic ClinVar variants found in the SNF8 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-48930497-T-G | not specified | Uncertain significance (Jun 21, 2022) | ||
17-48930553-G-C | not specified | Uncertain significance (Nov 09, 2021) | ||
17-48930558-C-T | not specified | Uncertain significance (Apr 07, 2023) | ||
17-48930566-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
17-48930569-GCCTGTAAGTC-TCCA | SNF8-associated disease • Neurodevelopmental disorder plus optic atrophy | Pathogenic (Dec 07, 2023) | ||
17-48931653-C-T | Aganglionic megacolon | Uncertain significance (May 16, 2019) | ||
17-48931659-C-A | SNF8-associated disease • Developmental and epileptic encephalopathy 115 | Pathogenic (Dec 07, 2023) | ||
17-48931710-C-T | SNF8-associated disease • Developmental and epileptic encephalopathy 115 | Pathogenic (Dec 07, 2023) | ||
17-48933239-T-C | not specified | Uncertain significance (Jun 13, 2024) | ||
17-48933268-G-T | SNF8-associated disease • Developmental and epileptic encephalopathy 115 | Pathogenic (Dec 07, 2023) | ||
17-48933347-C-G | SNF8-associated disease • Neurodevelopmental disorder plus optic atrophy | Pathogenic (Dec 07, 2023) | ||
17-48936186-C-T | not specified | Uncertain significance (May 29, 2024) | ||
17-48937065-C-T | SNF8-associated disease • Neurodevelopmental disorder plus optic atrophy • not specified | Conflicting classifications of pathogenicity (Jan 30, 2024) | ||
17-48937092-C-T | not specified | Uncertain significance (Oct 30, 2023) | ||
17-48940932-G-A | SNF8-associated disease • Developmental and epileptic encephalopathy 115 • Neurodevelopmental disorder plus optic atrophy | Pathogenic (Dec 07, 2023) | ||
17-48940948-T-A | not specified | Uncertain significance (Apr 23, 2024) | ||
17-48940975-G-A | not specified | Uncertain significance (Mar 04, 2024) | ||
17-48944685-G-A | not specified | Uncertain significance (Jan 04, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SNF8 | protein_coding | protein_coding | ENST00000502492 | 8 | 15802 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000457 | 0.969 | 125718 | 0 | 30 | 125748 | 0.000119 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.13 | 113 | 152 | 0.742 | 0.00000854 | 1675 |
Missense in Polyphen | 19 | 40.86 | 0.465 | 469 | ||
Synonymous | -0.331 | 66 | 62.7 | 1.05 | 0.00000381 | 500 |
Loss of Function | 1.91 | 8 | 16.3 | 0.489 | 8.21e-7 | 178 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000116 | 0.000116 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000435 | 0.000435 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000794 | 0.0000791 |
Middle Eastern | 0.000435 | 0.000435 |
South Asian | 0.000163 | 0.000163 |
Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation by participating in derepression of transcription by RNA polymerase II, possibly via its interaction with ELL. Required for degradation of both endocytosed EGF and EGFR, but not for the EGFR ligand-mediated internalization. It is also required for the degradation of CXCR4. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:17714434, ECO:0000269|PubMed:17959629, ECO:0000269|PubMed:18031739, ECO:0000269|PubMed:22660413}.;
- Pathway
- Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Endosomal Sorting Complex Required For Transport (ESCRT)
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.380
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.230
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.972
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snf8
- Phenotype
- homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;positive regulation of gene expression;regulation of multivesicular body size involved in endosome transport;endosomal transport;macroautophagy;endocytic recycling;multivesicular body assembly;regulation of protein catabolic process;protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;regulation of MAP kinase activity;early endosome to late endosome transport;positive regulation of protein catabolic process;regulation of protein complex stability;multivesicular body sorting pathway;positive regulation of exosomal secretion;regulation of viral budding via host ESCRT complex
- Cellular component
- ESCRT II complex;nucleus;nucleoplasm;transcription factor complex;cytoplasm;cytosol;plasma membrane;endosome membrane;membrane;late endosome membrane;perinuclear region of cytoplasm;recycling endosome;extracellular exosome
- Molecular function
- protein binding;protein C-terminus binding;transcription factor binding;channel regulator activity;protein homodimerization activity;protein N-terminus binding