SIPA1L2

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

Basic information

Region (hg38): 1:232397964-232630571

Links

ENSG00000116991 ∙ NCBI:57568 ∙ OMIM:611609 ∙ HGNC:23800 ∙ Uniprot:Q9P2F8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (73 variants)
• not provided (12 variants)

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	8	9
missense			70	4	1	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	70	5	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)
1-232402417-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)
1-232403478-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)
1-232415578-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)
1-232432400-A-C		not specified	Uncertain significance (Dec 16, 2023)
1-232432452-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-232439148-C-T		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sipa1l2

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