STAB1

stabilin 1, the group of Scavenger receptors

Basic information

Region (hg38): 3:52495338-52524495

Links

ENSG00000010327 ∙ NCBI:23166 ∙ OMIM:608560 ∙ HGNC:18628 ∙ Uniprot:Q9NY15 ∙ 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 STAB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAB1 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				10	6	16
missense			169	13	2	184
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding				1	1	2
Total	0	0	169	24	9

Variants in STAB1

This is a list of pathogenic ClinVar variants found in the STAB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52495427-G-A		not specified	Likely benign (Mar 28, 2024)
3-52501229-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-52501254-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-52501268-C-T		not specified	Uncertain significance (Oct 20, 2021)
3-52501269-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-52501661-C-G		not specified	Uncertain significance (Apr 20, 2023)
3-52501717-G-A		not specified	Uncertain significance (Aug 26, 2022)
3-52501744-C-T		not specified	Uncertain significance (May 08, 2023)
3-52502014-G-A		not specified	Uncertain significance (Jul 05, 2023)
3-52502020-G-A		not specified	Uncertain significance (Nov 07, 2022)
3-52502200-C-T			Likely benign (Aug 01, 2022)
3-52502205-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-52502210-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-52502648-C-T			Benign (Dec 31, 2019)
3-52502671-G-A			Uncertain significance (Dec 01, 2022)
3-52502994-C-T			Likely benign (Mar 01, 2023)
3-52503025-T-C		not specified	Uncertain significance (May 06, 2024)
3-52503070-T-A		not specified	Uncertain significance (Sep 29, 2023)
3-52503364-T-C		not specified	Uncertain significance (Aug 08, 2022)
3-52503392-C-G		not specified	Uncertain significance (Sep 23, 2023)
3-52503506-A-G		not specified	Uncertain significance (Dec 12, 2023)
3-52503512-C-T		not specified	Uncertain significance (May 04, 2023)
3-52503534-G-A			Likely benign (Apr 01, 2022)
3-52503549-G-C			Likely benign (Feb 09, 2018)
3-52503800-T-G		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAB1	protein_coding	protein_coding	ENST00000321725	69	29158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.68e-50	0.927	125376	0	370	125746	0.00147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	1478	1.60e+3	0.923	0.000104	16659
Missense in Polyphen		419	553.37	0.75719		6076
Synonymous	-1.82	727	667	1.09	0.0000459	5154
Loss of Function	3.60	102	149	0.682	0.00000795	1565

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00263	0.00262
Ashkenazi Jewish	0.00131	0.00129
East Asian	0.00136	0.00136
Finnish	0.000862	0.000786
European (Non-Finnish)	0.00200	0.00194
Middle Eastern	0.00136	0.00136
South Asian	0.000623	0.000621
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a scavenger receptor for acetylated low density lipoprotein. Binds to both Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. When inhibited in endothelial tube formation assays, there is a marked decrease in cell-cell interactions, suggesting a role in angiogenesis. Involved in the delivery of newly synthesized CHID1/SI-CLP from the biosynthetic compartment to the endosomal/lysosomal system. {ECO:0000269|PubMed:12077138, ECO:0000269|PubMed:16357325}.
• Pathway: Vesicle-mediated transport;Scavenging by Class H Receptors;Binding and Uptake of Ligands by Scavenger Receptors (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.0541
• rvis_EVS: -4.12
• rvis_percentile_EVS: 0.16

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.466
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stab1
• Phenotype: renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal 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); respiratory system phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: stab1
• Affected structure: vascular lymphangioblast
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: receptor-mediated endocytosis;inflammatory response;cell adhesion;cell-cell signaling;negative regulation of angiogenesis;defense response to bacterium;oxidation-reduction process
• Cellular component: plasma membrane;integral component of plasma membrane;endocytic vesicle membrane
• Molecular function: low-density lipoprotein particle receptor activity;scavenger receptor activity;calcium ion binding;protein binding;hyaluronic acid binding;protein disulfide oxidoreductase activity;low-density lipoprotein particle binding