SIPA1L2
Basic information
Region (hg38): 1:232397965-232630571
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 SIPA1L2 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 | 9 | |||||
missense | 97 | 104 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 97 | 7 | 10 |
Variants in SIPA1L2
This is a list of pathogenic ClinVar variants found in the SIPA1L2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-232399189-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
1-232402397-G-A | not specified | Uncertain significance (Dec 16, 2022) | ||
1-232402403-C-T | not specified | Uncertain significance (Apr 15, 2024) | ||
1-232402417-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
1-232402421-G-T | not specified | Uncertain significance (Apr 19, 2023) | ||
1-232402443-T-G | not specified | Uncertain significance (Aug 28, 2023) | ||
1-232402469-G-A | not specified | Uncertain significance (Apr 24, 2024) | ||
1-232403478-C-T | not specified | Uncertain significance (Feb 03, 2023) | ||
1-232403500-G-T | not specified | Uncertain significance (Feb 10, 2023) | ||
1-232403509-C-A | not specified | Uncertain significance (Dec 19, 2023) | ||
1-232403563-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
1-232404131-A-G | not specified | Uncertain significance (Dec 14, 2021) | ||
1-232415515-C-A | not specified | Uncertain significance (Mar 28, 2024) | ||
1-232415578-C-T | not specified | Uncertain significance (Oct 17, 2023) | ||
1-232415579-G-A | Benign (Mar 02, 2018) | |||
1-232425604-T-G | not specified | Uncertain significance (Nov 17, 2023) | ||
1-232425622-C-A | not specified | Uncertain significance (Jul 06, 2021) | ||
1-232425774-G-A | Benign (Sep 28, 2017) | |||
1-232428492-C-G | not specified | Uncertain significance (Aug 04, 2023) | ||
1-232428518-T-C | not specified | Likely benign (Feb 22, 2023) | ||
1-232428542-T-G | Likely benign (Nov 01, 2022) | |||
1-232432238-C-T | Benign (Dec 31, 2019) | |||
1-232432248-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
1-232432308-C-T | not specified | Uncertain significance (Dec 09, 2023) | ||
1-232432362-C-T | not specified | Uncertain significance (Oct 27, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SIPA1L2 | protein_coding | protein_coding | ENST00000366630 | 21 | 163594 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.992 | 0.00785 | 124986 | 0 | 20 | 125006 | 0.0000800 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.46 | 877 | 1.01e+3 | 0.870 | 0.0000600 | 11314 |
Missense in Polyphen | 316 | 433.19 | 0.72947 | 4921 | ||
Synonymous | -1.01 | 446 | 420 | 1.06 | 0.0000284 | 3421 |
Loss of Function | 6.60 | 14 | 76.2 | 0.184 | 0.00000460 | 829 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000159 | 0.000156 |
Ashkenazi Jewish | 0.0000994 | 0.0000993 |
East Asian | 0.000223 | 0.000222 |
Finnish | 0.0000928 | 0.0000928 |
European (Non-Finnish) | 0.0000533 | 0.0000529 |
Middle Eastern | 0.000223 | 0.000222 |
South Asian | 0.0000981 | 0.0000980 |
Other | 0.000166 | 0.000164 |
dbNSFP
Source:
- Pathway
- Rap1 signaling pathway - Homo sapiens (human)
(Consensus)
Intolerance Scores
- loftool
- 0.134
- rvis_EVS
- -1.31
- rvis_percentile_EVS
- 4.87
Haploinsufficiency Scores
- pHI
- 0.235
- hipred
- Y
- hipred_score
- 0.544
- ghis
- 0.414
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.224
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sipa1l2
- Phenotype
Gene ontology
- Biological process
- biological_process;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
- Cellular component
- cellular_component
- Molecular function
- GTPase activator activity