SMNDC1
Basic information
Region (hg38): 10:110290730-110304938
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 SMNDC1 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in SMNDC1
This is a list of pathogenic ClinVar variants found in the SMNDC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-110295299-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
| 10-110297593-C-G | not specified | Uncertain significance (Dec 21, 2022) | ||
| 10-110297604-T-G | not specified | Uncertain significance (Nov 14, 2023) | ||
| 10-110297649-C-G | not specified | Uncertain significance (Jul 07, 2022) | ||
| 10-110297682-C-T | not specified | Uncertain significance (Nov 07, 2023) | ||
| 10-110303572-C-T | not specified | Uncertain significance (Jun 16, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMNDC1 | protein_coding | protein_coding | ENST00000369603 | 5 | 14222 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.638 | 0.361 | 122810 | 0 | 2 | 122812 | 0.00000814 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.48 | 40 | 115 | 0.348 | 0.00000520 | 1563 |
| Missense in Polyphen | 4 | 41.539 | 0.096295 | 587 | ||
| Synonymous | 1.32 | 30 | 40.7 | 0.737 | 0.00000201 | 415 |
| Loss of Function | 2.66 | 2 | 11.9 | 0.168 | 4.99e-7 | 172 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000107 | 0.000101 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000954 | 0.00000892 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Necessary for spliceosome assembly. Overexpression causes apoptosis. {ECO:0000269|PubMed:11331295, ECO:0000269|PubMed:11331595, ECO:0000269|PubMed:9817934}.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.169
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.400
- hipred
- Y
- hipred_score
- 0.734
- ghis
- 0.694
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smndc1
- Phenotype
Gene ontology
- Biological process
- RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;apoptotic process
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;cytoplasm;Cajal body;nuclear speck
- Molecular function
- RNA binding;protein binding