CYSTM1
Basic information
Region (hg38): 5:140175156-140282052
Previous symbols: [ "C5orf32" ]
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 CYSTM1 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 CYSTM1
This is a list of pathogenic ClinVar variants found in the CYSTM1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-140194584-G-C | not specified | Uncertain significance (Aug 14, 2023) | ||
| 5-140194584-G-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| 5-140194613-G-A | not specified | Uncertain significance (May 09, 2023) | ||
| 5-140194622-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
| 5-140243329-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 5-140243343-C-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 5-140243350-C-T | not specified | Uncertain significance (Nov 19, 2022) | ||
| 5-140246035-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
| 5-140281490-C-G | not specified | Uncertain significance (Jun 01, 2023) | ||
| 5-140281512-T-G | not specified | Uncertain significance (Oct 22, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CYSTM1 | protein_coding | protein_coding | ENST00000261811 | 2 | 107411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.423 | 0.547 | 125508 | 0 | 6 | 125514 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.668 | 41 | 54.9 | 0.746 | 0.00000263 | 610 |
| Missense in Polyphen | ||||||
| Synonymous | 0.0335 | 20 | 20.2 | 0.991 | 0.00000113 | 195 |
| Loss of Function | 1.72 | 1 | 5.27 | 0.190 | 2.25e-7 | 56 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000616 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.144
- hipred
- N
- hipred_score
- 0.412
- ghis
- 0.535
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cystm1
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- biological_process;neutrophil degranulation
- Cellular component
- plasma membrane;integral component of membrane;extracellular exosome;tertiary granule membrane
- Molecular function
- molecular_function