SGIP1

SH3GL interacting endocytic adaptor 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:66533266-66751139

Links

ENSG00000118473 ∙ NCBI:84251 ∙ OMIM:611540 ∙ HGNC:25412 ∙ Uniprot:Q9BQI5 ∙ 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 SGIP1 gene.

• Inborn genetic diseases (28 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGIP1 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	1

Variants in SGIP1

This is a list of pathogenic ClinVar variants found in the SGIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-66534362-A-G		not specified	Uncertain significance (Dec 07, 2021)
1-66625858-C-T		not specified	Uncertain significance (Jan 22, 2024)
1-66625876-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-66625877-G-C		not specified	Uncertain significance (Apr 09, 2022)
1-66625882-C-T		not specified	Uncertain significance (Jun 07, 2023)
1-66633084-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-66635959-G-A		not specified	Uncertain significance (Jun 21, 2023)
1-66639810-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-66643619-A-G		not specified	Uncertain significance (Dec 09, 2023)
1-66643649-T-C		not specified	Uncertain significance (Aug 28, 2023)
1-66667534-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-66667537-G-T		not specified	Uncertain significance (Jun 22, 2021)
1-66671016-T-C		not specified	Uncertain significance (Sep 20, 2023)
1-66671968-G-C		not specified	Uncertain significance (Oct 10, 2023)
1-66677027-T-G		not specified	Uncertain significance (Aug 15, 2023)
1-66677081-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-66677090-A-G		not specified	Uncertain significance (Jul 12, 2023)
1-66679749-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-66681892-G-A		not specified	Likely benign (Sep 20, 2023)
1-66681946-G-T		not specified	Uncertain significance (Apr 28, 2022)
1-66681965-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-66682006-A-G		not specified	Uncertain significance (Jul 12, 2023)
1-66682007-C-T		not specified	Uncertain significance (Jan 12, 2024)
1-66682057-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-66682123-C-T		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGIP1	protein_coding	protein_coding	ENST00000371037	25	214917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000308	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	401	465	0.862	0.0000250	5317
Missense in Polyphen		142	178.02	0.79767		1985
Synonymous	0.599	160	170	0.942	0.00000963	1681
Loss of Function	5.81	4	47.0	0.0852	0.00000239	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000529	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in clathrin-mediated endocytosis. Has both a membrane binding/tubulating activity and the ability to recruit proteins essential to the formation of functional clathrin-coated pits. Has a preference for membranes enriched in phosphatidylserine and phosphoinositides and is required for the endocytosis of the transferrin receptor. May also bind tubulin. May play a role in the regulation of energy homeostasis. {ECO:0000250|UniProtKB:Q8VD37}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.0870

Intolerance Scores

• loftool: 0.422
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.554
• hipred: Y
• hipred_score: 0.656
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgip1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: response to dietary excess;positive regulation of receptor-mediated endocytosis;clathrin coat assembly;membrane organization;clathrin-dependent endocytosis;energy homeostasis;plasma membrane tubulation;positive regulation of feeding behavior
• Cellular component: cytoplasm;cytosol;cytoskeleton;plasma membrane;clathrin-coated pit;AP-2 adaptor complex;clathrin-coated vesicle
• Molecular function: protein binding;phospholipid binding;microtubule binding;cytoskeletal protein binding;tubulin binding;SH3 domain binding