SCARF1

scavenger receptor class F member 1, the group of Scavenger receptors

Basic information

Region (hg38): 17:1633857-1645744

Links

ENSG00000074660 ∙ NCBI:8578 ∙ OMIM:607873 ∙ HGNC:16820 ∙ Uniprot:Q14162 ∙ 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 SCARF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARF1 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			54	5	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	5	2

Variants in SCARF1

This is a list of pathogenic ClinVar variants found in the SCARF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1634789-A-G			Benign (Jan 08, 2018)
17-1634845-C-G		not specified	Uncertain significance (Mar 23, 2022)
17-1634853-G-C		not specified	Uncertain significance (May 24, 2023)
17-1634949-G-A		not specified	Likely benign (Jun 28, 2022)
17-1634954-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-1634987-T-C		not specified	Likely benign (Jul 09, 2021)
17-1635017-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-1635018-G-A		not specified	Uncertain significance (Sep 01, 2021)
17-1635024-G-A		not specified	Uncertain significance (Oct 26, 2021)
17-1635039-G-A		not specified	Uncertain significance (Jun 09, 2022)
17-1635056-G-A		not specified	Uncertain significance (Jan 03, 2024)
17-1635080-A-C		not specified	Uncertain significance (Mar 01, 2024)
17-1635081-C-A		not specified	Uncertain significance (Dec 07, 2023)
17-1635082-C-G		not specified	Uncertain significance (Oct 04, 2022)
17-1635120-G-A		not specified	Uncertain significance (Oct 06, 2022)
17-1635246-T-G		not specified	Uncertain significance (Jun 30, 2022)
17-1635270-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-1635362-C-T		not specified	Likely benign (Oct 03, 2022)
17-1635389-C-G		not specified	Uncertain significance (Aug 01, 2022)
17-1635443-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-1635455-G-A		not specified	Uncertain significance (Apr 26, 2024)
17-1635471-C-G		not specified	Uncertain significance (Feb 23, 2023)
17-1635485-G-A		not specified	Uncertain significance (May 24, 2023)
17-1635549-C-T		not specified	Uncertain significance (Apr 18, 2023)
17-1636769-A-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARF1	protein_coding	protein_coding	ENST00000263071	11	11890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.29e-7	0.998	125586	1	157	125744	0.000628

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	370	437	0.847	0.0000268	5254
Missense in Polyphen		92	113.74	0.80887		1398
Synonymous	-1.01	208	190	1.09	0.0000130	1713
Loss of Function	2.80	16	33.5	0.478	0.00000197	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000809	0.000802
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00136	0.00120
European (Non-Finnish)	0.00102	0.000844
Middle Eastern	0.00	0.00
South Asian	0.000426	0.000425
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). Mediates heterophilic interactions, suggesting a function as adhesion protein. Plays a role in the regulation of neurite-like outgrowth (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class F Receptors (Consensus)

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 2.34
• rvis_percentile_EVS: 98.4

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.270
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0443

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scarf1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; normal phenotype; 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); hematopoietic system phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: cholesterol catabolic process;receptor-mediated endocytosis;cell adhesion;positive regulation of neuron projection development;neuron remodeling;dendrite development;positive regulation of axon regeneration
• Cellular component: plasma membrane;integral component of membrane;endocytic vesicle membrane
• Molecular function: transmembrane signaling receptor activity;scavenger receptor activity;low-density lipoprotein particle binding