SCARA3

scavenger receptor class A member 3, the group of MicroRNA protein coding host genes|Scavenger receptors

Basic information

Region (hg38): 8:27633867-27676776

Links

ENSG00000168077 ∙ NCBI:51435 ∙ OMIM:602728 ∙ HGNC:19000 ∙ Uniprot:Q6AZY7 ∙ 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 SCARA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARA3 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						0
missense			34	6		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	6	0

Variants in SCARA3

This is a list of pathogenic ClinVar variants found in the SCARA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-27649708-C-T		not specified	Uncertain significance (Jun 17, 2024)
8-27649716-G-A		not specified	Uncertain significance (Jan 17, 2023)
8-27649737-G-A		not specified	Uncertain significance (Jul 26, 2021)
8-27649741-C-T		not specified	Uncertain significance (Apr 19, 2024)
8-27649763-C-A		not specified	Likely benign (Apr 13, 2022)
8-27649777-C-T		SCARA3-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 16, 2023)
8-27651510-C-T		not specified	Uncertain significance (Mar 17, 2023)
8-27651523-G-A		not specified	Uncertain significance (Dec 06, 2022)
8-27651567-C-T		not specified	Uncertain significance (Dec 20, 2023)
8-27656808-G-A		not specified	Uncertain significance (Aug 08, 2023)
8-27658499-C-T		not specified	Likely benign (Jan 10, 2023)
8-27658507-C-G		not specified	Uncertain significance (Apr 07, 2023)
8-27658529-A-G		not specified	Uncertain significance (Apr 07, 2023)
8-27658547-G-A		not specified	Uncertain significance (Jun 05, 2024)
8-27658591-A-G		not specified	Uncertain significance (Jun 10, 2024)
8-27658606-C-G		not specified	Uncertain significance (Aug 23, 2021)
8-27658739-C-T		not specified	Uncertain significance (Feb 17, 2023)
8-27658766-C-A		not specified	Uncertain significance (Apr 15, 2024)
8-27658779-C-G		not specified	Uncertain significance (Sep 29, 2023)
8-27658780-C-T		not specified	Uncertain significance (Sep 28, 2021)
8-27658803-G-C		not specified	Uncertain significance (Jul 08, 2022)
8-27658843-T-C		not specified	Uncertain significance (Aug 17, 2022)
8-27658864-G-A		not specified	Uncertain significance (Mar 30, 2024)
8-27658957-A-G		not specified	Likely benign (Nov 08, 2022)
8-27658960-G-A		not specified	Likely benign (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARA3	protein_coding	protein_coding	ENST00000301904	6	42909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.98e-8	0.758	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	333	346	0.962	0.0000209	3880
Missense in Polyphen		113	120.56	0.9373		1323
Synonymous	-1.22	174	155	1.13	0.0000104	1291
Loss of Function	1.40	15	22.1	0.679	0.00000118	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000547	0.000539
Ashkenazi Jewish	0.00218	0.00218
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000360	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to protect cells by scavenging oxidative molecules or harmful products of oxidation. {ECO:0000269|PubMed:9580669}.

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.64

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.282
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.272

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scara3

Gene ontology

• Biological process: complement activation, lectin pathway;growth plate cartilage chondrocyte morphogenesis;receptor-mediated endocytosis;response to oxidative stress;UV protection;toll-like receptor 3 signaling pathway
• Cellular component: Golgi membrane;collagen trimer;extracellular space;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;extracellular matrix
• Molecular function: scavenger receptor activity;calcium ion binding;protein binding;mannose binding