MSC
Basic information
Region (hg38): 8:71841560-71844412
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 MSC 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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in MSC
This is a list of pathogenic ClinVar variants found in the MSC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-71842678-A-G | not specified | Uncertain significance (Apr 20, 2024) | ||
| 8-71842692-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 8-71842736-G-T | not specified | Uncertain significance (Apr 28, 2023) | ||
| 8-71843664-T-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 8-71843744-C-G | not specified | Uncertain significance (Aug 08, 2022) | ||
| 8-71843827-C-A | not specified | Uncertain significance (Jun 28, 2023) | ||
| 8-71843875-C-T | not specified | Uncertain significance (Feb 08, 2023) | ||
| 8-71843887-T-C | not specified | Uncertain significance (Nov 22, 2023) | ||
| 8-71843920-C-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 8-71843938-C-T | not specified | Uncertain significance (Apr 13, 2022) | ||
| 8-71843953-G-A | not specified | Uncertain significance (Dec 20, 2021) | ||
| 8-71844089-G-C | Likely benign (May 01, 2022) | |||
| 8-71844091-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
| 8-71844142-C-G | not specified | Uncertain significance (Feb 03, 2022) | ||
| 8-71844158-A-T | not specified | Uncertain significance (Mar 19, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MSC | protein_coding | protein_coding | ENST00000325509 | 2 | 2920 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0247 | 0.793 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0154 | 117 | 117 | 0.996 | 0.00000534 | 1280 |
| Missense in Polyphen | 32 | 44.274 | 0.72278 | 455 | ||
| Synonymous | -0.466 | 56 | 51.7 | 1.08 | 0.00000249 | 451 |
| Loss of Function | 0.988 | 3 | 5.50 | 0.545 | 2.34e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription repressor capable of inhibiting the transactivation capability of TCF3/E47. May play a role in regulating antigen-dependent B-cell differentiation.;
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- 0.256
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 66.57
Haploinsufficiency Scores
- pHI
- 0.325
- hipred
- Y
- hipred_score
- 0.585
- ghis
- 0.509
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- 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
- Msc
- Phenotype
- craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- msc
- Affected structure
- head muscle
- Phenotype tag
- abnormal
- Phenotype quality
- hypoplastic
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;branchiomeric skeletal muscle development;roof of mouth development;diaphragm development;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;protein dimerization activity