SIPA1L2

signal induced proliferation associated 1 like 2, the group of PDZ domain containing

Basic information

Region (hg38): 1:232397965-232630571

Links

ENSG00000116991NCBI:57568OMIM:611609HGNC:23800Uniprot:Q9P2F8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SIPA1L2 gene.

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
1
clinvar
8
clinvar
9
missense
97
clinvar
6
clinvar
1
clinvar
104
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)3162425
1-232402397-G-A not specified Uncertain significance (Dec 16, 2022)2392518
1-232402403-C-T not specified Uncertain significance (Apr 15, 2024)3318592
1-232402417-C-T not specified Uncertain significance (Oct 04, 2022)2316849
1-232402421-G-T not specified Uncertain significance (Apr 19, 2023)2539071
1-232402443-T-G not specified Uncertain significance (Aug 28, 2023)2621696
1-232402469-G-A not specified Uncertain significance (Apr 24, 2024)3318593
1-232403478-C-T not specified Uncertain significance (Feb 03, 2023)2459921
1-232403500-G-T not specified Uncertain significance (Feb 10, 2023)2458092
1-232403509-C-A not specified Uncertain significance (Dec 19, 2023)3162424
1-232403563-C-T not specified Uncertain significance (Jan 09, 2024)3162423
1-232404131-A-G not specified Uncertain significance (Dec 14, 2021)2266759
1-232415515-C-A not specified Uncertain significance (Mar 28, 2024)3318590
1-232415578-C-T not specified Uncertain significance (Oct 17, 2023)3162422
1-232415579-G-A Benign (Mar 02, 2018)714105
1-232425604-T-G not specified Uncertain significance (Nov 17, 2023)3162421
1-232425622-C-A not specified Uncertain significance (Jul 06, 2021)2343601
1-232425774-G-A Benign (Sep 28, 2017)718930
1-232428492-C-G not specified Uncertain significance (Aug 04, 2023)2616397
1-232428518-T-C not specified Likely benign (Feb 22, 2023)2466594
1-232428542-T-G Likely benign (Nov 01, 2022)2640082
1-232432238-C-T Benign (Dec 31, 2019)784976
1-232432248-C-T not specified Uncertain significance (Nov 14, 2023)3162420
1-232432308-C-T not specified Uncertain significance (Dec 09, 2023)3162419
1-232432362-C-T not specified Uncertain significance (Oct 27, 2022)2352556

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SIPA1L2protein_codingprotein_codingENST00000366630 21163594
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9920.007851249860201250060.0000800
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.468771.01e+30.8700.000060011314
Missense in Polyphen316433.190.729474921
Synonymous-1.014464201.060.00002843421
Loss of Function6.601476.20.1840.00000460829

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001590.000156
Ashkenazi Jewish0.00009940.0000993
East Asian0.0002230.000222
Finnish0.00009280.0000928
European (Non-Finnish)0.00005330.0000529
Middle Eastern0.0002230.000222
South Asian0.00009810.0000980
Other0.0001660.000164

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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