C1orf105
Basic information
Region (hg38): 1:172420685-172468831
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Glycosylphosphatidylinositol biosynthesis defect 16 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf105 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 | 2 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 43 | 60 | ||||
Total | 1 | 4 | 45 | 8 | 4 |
Variants in C1orf105
This is a list of pathogenic ClinVar variants found in the C1orf105 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-172441742-C-A | Glycosylphosphatidylinositol biosynthesis defect 16 | Uncertain significance (Sep 22, 2024) | ||
1-172441758-T-G | not specified | Uncertain significance (Aug 30, 2022) | ||
1-172441762-T-C | Likely benign (Feb 01, 2023) | |||
1-172441764-C-A | Glycosylphosphatidylinositol biosynthesis defect 16 | Pathogenic (Nov 29, 2022) | ||
1-172441773-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
1-172441811-C-T | Glycosylphosphatidylinositol biosynthesis defect 16 | Uncertain significance (Dec 28, 2022) | ||
1-172441827-G-A | Glycosylphosphatidylinositol biosynthesis defect 16 | Benign (Jan 31, 2024) | ||
1-172441832-A-G | not specified | Uncertain significance (Dec 06, 2024) | ||
1-172441853-A-G | not specified | Uncertain significance (Aug 20, 2024) | ||
1-172441884-T-C | Glycosylphosphatidylinositol biosynthesis defect 16 | Uncertain significance (Nov 15, 2018) | ||
1-172441889-G-C | not specified | Uncertain significance (Sep 04, 2024) | ||
1-172441946-C-T | not specified | Uncertain significance (Apr 24, 2024) | ||
1-172441947-G-A | Benign/Likely benign (Oct 01, 2024) | |||
1-172441964-A-G | Non-immune hydrops fetalis • Glycosylphosphatidylinositol biosynthesis defect 16 | Conflicting classifications of pathogenicity (Mar 17, 2024) | ||
1-172441979-A-G | Uncertain significance (Oct 01, 2022) | |||
1-172441988-A-C | not specified | Uncertain significance (Feb 27, 2024) | ||
1-172441988-A-G | Glycosylphosphatidylinositol biosynthesis defect 16 | Likely pathogenic (Oct 15, 2018) | ||
1-172442018-A-C | not specified | Uncertain significance (Sep 25, 2024) | ||
1-172442030-T-C | not specified | Uncertain significance (May 06, 2024) | ||
1-172442039-C-T | Uncertain significance (Aug 02, 2022) | |||
1-172442043-G-T | not specified | Uncertain significance (Aug 27, 2024) | ||
1-172442049-G-A | Glycosylphosphatidylinositol biosynthesis defect 16 • not specified | Uncertain significance (Oct 06, 2024) | ||
1-172442057-A-C | Glycosylphosphatidylinositol biosynthesis defect 16 | Likely pathogenic (Oct 15, 2018) | ||
1-172442066-G-C | not specified | Uncertain significance (Sep 24, 2021) | ||
1-172442090-G-A | Uncertain significance (Oct 04, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
C1orf105 | protein_coding | protein_coding | ENST00000367727 | 7 | 48144 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000110 | 0.371 | 111498 | 599 | 13630 | 125727 | 0.0583 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.350 | 84 | 93.5 | 0.898 | 0.00000443 | 1199 |
Missense in Polyphen | 8 | 6.002 | 1.3329 | 69 | ||
Synonymous | 0.859 | 27 | 33.3 | 0.811 | 0.00000166 | 332 |
Loss of Function | 0.295 | 8 | 8.95 | 0.894 | 3.77e-7 | 118 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0667 | 0.0659 |
Ashkenazi Jewish | 0.0965 | 0.0942 |
East Asian | 0.00104 | 0.000489 |
Finnish | 0.118 | 0.116 |
European (Non-Finnish) | 0.0655 | 0.0638 |
Middle Eastern | 0.00104 | 0.000489 |
South Asian | 0.0684 | 0.0635 |
Other | 0.0751 | 0.0729 |
dbNSFP
Source:
Intolerance Scores
- loftool
- 0.784
- rvis_EVS
- 0.73
- rvis_percentile_EVS
- 85.98
Haploinsufficiency Scores
- pHI
- 0.0532
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- 4930558K02Rik
- Phenotype
Gene ontology
- Biological process
- Cellular component
- Molecular function
- protein binding