SIPA1L1

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

Basic information

Region (hg38): 14:71320449-71741229

Links

ENSG00000197555 ∙ NCBI:26037 ∙ OMIM:617504 ∙ HGNC:20284 ∙ Uniprot:O43166 ∙ 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 SIPA1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIPA1L1 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				7	4	11
missense			92	2	2	96
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	92	9	6

Variants in SIPA1L1

This is a list of pathogenic ClinVar variants found in the SIPA1L1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-71587889-G-A		not specified	Uncertain significance (Feb 11, 2022)
14-71587981-C-T		not specified	Uncertain significance (Oct 03, 2023)
14-71587985-G-A		not specified	Uncertain significance (Mar 03, 2022)
14-71587990-C-T		not specified	Uncertain significance (Nov 27, 2023)
14-71587991-G-A			Benign (Mar 29, 2018)
14-71588000-A-T		not specified	Uncertain significance (Mar 01, 2024)
14-71588038-C-A			Benign (Jun 08, 2018)
14-71588042-C-A			Likely benign (Nov 01, 2023)
14-71588067-A-G		not specified	Uncertain significance (Aug 02, 2021)
14-71588069-C-A		not specified	Uncertain significance (Nov 10, 2022)
14-71588153-G-A		not specified	Uncertain significance (Oct 26, 2022)
14-71588263-A-G		not specified	Uncertain significance (Apr 13, 2022)
14-71588273-G-T		not specified	Uncertain significance (Jun 10, 2022)
14-71588300-C-G		not specified	Uncertain significance (Dec 07, 2021)
14-71588300-C-T		not specified	Uncertain significance (Aug 02, 2022)
14-71588307-G-A			Likely benign (Aug 01, 2022)
14-71588324-C-T		not specified	Uncertain significance (Jun 28, 2023)
14-71588361-C-G			Benign (Mar 29, 2018)
14-71588369-C-G		not specified	Uncertain significance (Oct 17, 2023)
14-71588404-A-G		not specified	Uncertain significance (Nov 14, 2023)
14-71588468-G-T		not specified	Uncertain significance (Dec 21, 2023)
14-71588504-C-T		not specified	Uncertain significance (Dec 04, 2021)
14-71588545-T-G		not specified	Uncertain significance (Jan 23, 2024)
14-71588596-A-C		not specified	Uncertain significance (May 02, 2024)
14-71588618-C-T		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIPA1L1	protein_coding	protein_coding	ENST00000555818	21	420781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.06e-8	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.98	763	1.03e+3	0.739	0.0000596	11852
Missense in Polyphen		304	473.47	0.64206		5474
Synonymous	-0.0568	402	401	1.00	0.0000241	3581
Loss of Function	7.49	7	78.7	0.0890	0.00000477	888

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates the GTPase activity of RAP2A. Promotes reorganization of the actin cytoskeleton and recruits DLG4 to F- actin. Contributes to the regulation of dendritic spine morphogenesis (By similarity). {ECO:0000250}.
• Pathway: Rap1 signaling pathway - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: -2.73
• rvis_percentile_EVS: 0.7

Haploinsufficiency Scores

• pHI: 0.536
• hipred: Y
• hipred_score: 0.728
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.728

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sipa1l1

Gene ontology

• Biological process: biological_process;actin cytoskeleton reorganization;regulation of GTPase activity;ephrin receptor signaling pathway;regulation of synaptic plasticity;regulation of axonogenesis;regulation of small GTPase mediated signal transduction;regulation of dendritic spine morphogenesis;activation of GTPase activity
• Cellular component: cellular_component;cytoplasm;cytoskeleton;postsynaptic density;cell junction;dendritic spine;postsynaptic membrane
• Molecular function: molecular_function;GTPase activator activity;ephrin receptor binding