SND1
Basic information
Region (hg38): 7:127652194-128092609
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SND1 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 | 10 | 14 | ||||
missense | 41 | 42 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | 2 | |||
non coding | 26 | 31 | ||||
Total | 0 | 0 | 68 | 12 | 9 |
Variants in SND1
This is a list of pathogenic ClinVar variants found in the SND1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC | Benign (Dec 31, 2019) | |||
7-127652388-G-C | Likely benign (Oct 23, 2018) | |||
7-127652393-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
7-127652422-C-A | not specified | Uncertain significance (May 30, 2024) | ||
7-127652426-C-A | not specified | Uncertain significance (Dec 22, 2023) | ||
7-127686609-G-A | Likely benign (Apr 11, 2018) | |||
7-127686631-A-T | SND1-related disorder | Uncertain significance (Mar 25, 2024) | ||
7-127686636-T-A | Likely benign (Aug 03, 2017) | |||
7-127686653-G-A | Teratoma | Uncertain significance (Jan 01, 2023) | ||
7-127686663-T-A | Likely benign (May 04, 2018) | |||
7-127686728-C-T | not specified | Uncertain significance (May 04, 2022) | ||
7-127694891-A-G | not specified | Uncertain significance (Jun 18, 2021) | ||
7-127694893-G-A | Likely benign (Dec 27, 2018) | |||
7-127698952-A-C | not specified | Uncertain significance (Aug 15, 2023) | ||
7-127701159-C-T | Benign (Dec 31, 2019) | |||
7-127701188-T-G | not specified | Uncertain significance (Jan 19, 2024) | ||
7-127701240-G-A | not specified | Uncertain significance (Nov 08, 2022) | ||
7-127701242-T-G | not specified | Uncertain significance (May 01, 2022) | ||
7-127702457-C-T | Likely benign (May 16, 2018) | |||
7-127702504-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
7-127703235-T-A | not specified | Uncertain significance (Jan 06, 2023) | ||
7-127703300-A-G | not specified | Uncertain significance (Feb 21, 2024) | ||
7-127704846-A-G | not specified | Uncertain significance (Jan 25, 2023) | ||
7-127704856-G-A | SND1-related disorder | Likely benign (Jul 20, 2020) | ||
7-127704900-T-G | not specified | Uncertain significance (Jan 31, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SND1 | protein_coding | protein_coding | ENST00000354725 | 24 | 440428 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.982 | 0.0179 | 125731 | 0 | 17 | 125748 | 0.0000676 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.39 | 334 | 560 | 0.596 | 0.0000338 | 5894 |
Missense in Polyphen | 84 | 204.25 | 0.41127 | 1989 | ||
Synonymous | 1.48 | 186 | 214 | 0.871 | 0.0000128 | 1824 |
Loss of Function | 5.72 | 10 | 56.4 | 0.177 | 0.00000337 | 592 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000579 | 0.0000579 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000186 | 0.000185 |
European (Non-Finnish) | 0.0000617 | 0.0000615 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000980 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Endonuclease that mediates miRNA decay of both protein- free and AGO2-loaded miRNAs (PubMed:28546213, PubMed:18453631). As part of its function in miRNA decay, regulates mRNAs involved in G1-to-S phase transition (PubMed:28546213). Functions as a bridging factor between STAT6 and the basal transcription factor (PubMed:12234934). Plays a role in PIM1 regulation of MYB activity (PubMed:9809063). Functions as a transcriptional coactivator for STAT5 (By similarity). {ECO:0000250|UniProtKB:Q78PY7, ECO:0000269|PubMed:12234934, ECO:0000269|PubMed:18453631, ECO:0000269|PubMed:28546213, ECO:0000269|PubMed:9809063}.;
- Pathway
- Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Disease;C-MYB transcription factor network;IL4;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.521
- rvis_EVS
- -1.06
- rvis_percentile_EVS
- 7.48
Haploinsufficiency Scores
- pHI
- 0.739
- hipred
- Y
- hipred_score
- 0.774
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snd1
- Phenotype
Gene ontology
- Biological process
- osteoblast differentiation;RNA catabolic process;regulation of cell cycle process;miRNA catabolic process;viral process;gene silencing by RNA;RNA phosphodiester bond hydrolysis, endonucleolytic;regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;cytoplasm;cytosol;membrane;RISC complex;melanosome;extracellular exosome;dense body
- Molecular function
- transcription coregulator activity;RNA binding;nuclease activity;endonuclease activity;endoribonuclease activity;protein binding;cadherin binding;RISC complex binding