SIPA1

signal-induced proliferation-associated 1, the group of PDZ domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:65638101-65650918

Links

ENSG00000213445 ∙ NCBI:6494 ∙ OMIM:602180 ∙ HGNC:10885 ∙ Uniprot:Q96FS4 ∙ 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 SIPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIPA1 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	1
missense			64	4	3	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	4	4

Variants in SIPA1

This is a list of pathogenic ClinVar variants found in the SIPA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65640931-T-C		not specified	Uncertain significance (Jul 12, 2022)
11-65640937-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-65640946-G-T		not specified	Uncertain significance (Mar 29, 2022)
11-65640956-G-A		not specified	Uncertain significance (Mar 13, 2023)
11-65640988-C-T		not specified	Uncertain significance (Dec 04, 2023)
11-65641033-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-65641060-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-65641070-T-C		not specified	Uncertain significance (Dec 19, 2022)
11-65641087-G-A		not specified	Uncertain significance (Jun 04, 2024)
11-65641096-G-A		not specified	Uncertain significance (Aug 14, 2023)
11-65641132-C-T		not specified	Uncertain significance (Jan 19, 2022)
11-65641138-C-G		not specified	Uncertain significance (Feb 16, 2023)
11-65641142-G-A		not specified	Uncertain significance (May 18, 2022)
11-65641158-C-G		not specified	Uncertain significance (May 11, 2022)
11-65641180-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-65641237-G-T			Benign (Apr 06, 2018)
11-65641259-C-A		not specified	Uncertain significance (Dec 18, 2023)
11-65641276-T-C		not specified	Uncertain significance (Jul 13, 2022)
11-65641288-A-G		Esophageal atresia;Pyloric stenosis	Uncertain significance (May 22, 2019)
11-65641357-C-G		not specified	Uncertain significance (Mar 25, 2024)
11-65641388-C-T		not specified	Uncertain significance (Jun 05, 2024)
11-65641567-G-T		not specified	Uncertain significance (Jun 04, 2024)
11-65642484-A-G		not specified	Uncertain significance (Dec 15, 2023)
11-65642575-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-65644972-G-C		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIPA1	protein_coding	protein_coding	ENST00000394224	15	12834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00458	0.995	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	445	617	0.721	0.0000423	6469
Missense in Polyphen		139	240.87	0.57707		2460
Synonymous	1.94	237	278	0.852	0.0000196	2310
Loss of Function	3.83	11	35.7	0.308	0.00000176	411

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the nuclear Ras-related regulatory proteins Rap1 and Rap2 in vitro, converting them to the putatively inactive GDP-bound state (PubMed:9346962). Affects cell cycle progression (By similarity). {ECO:0000250|UniProtKB:P46062, ECO:0000269|PubMed:9346962}.
• Pathway: Rap1 signaling pathway - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);MAPK Cascade;Immune System;Rap1 signalling;Adaptive Immune System;PDGFR-beta signaling pathway (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.15

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.520
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.818

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sipa1
• Phenotype: immune system phenotype; hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: cytoskeleton organization;negative regulation of cell adhesion;signal transduction;cell population proliferation;negative regulation of cell growth;intracellular signal transduction;cellular response to water deprivation;positive regulation of GTPase activity;negative regulation of cell cycle;regulation of small GTPase mediated signal transduction
• Cellular component: nucleus;cytosol;membrane;transport vesicle;protein-containing complex;perinuclear region of cytoplasm
• Molecular function: GTPase activator activity;protein binding;protein C-terminus binding