SCARF2

scavenger receptor class F member 2, the group of Scavenger receptors

Basic information

Region (hg38): 22:20424584-20437826

Links

ENSG00000244486 ∙ ∙ OMIM:613619 ∙ HGNC:19869 ∙ Uniprot:Q96GP6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• van den Ende-Gupta syndrome (Definitive), mode of inheritance: AR
• van den Ende-Gupta syndrome (Limited), mode of inheritance: AR
• van den Ende-Gupta syndrome (Supportive), mode of inheritance: AR
• van den Ende-Gupta syndrome (Moderate), mode of inheritance: AR
• van den Ende-Gupta syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Van den Ende-Gupta syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Ophthalmologic	20887961; 23808541; 24478002

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCARF2 gene.

• Van den Ende-Gupta syndrome (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARF2 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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				16	6	22
missense		2	106	5	7	120
nonsense	1					1
start loss		1				1
frameshift	2				6	8
splice donor/acceptor (+/-2bp)						0
Total	3	3	106	21	19

Highest pathogenic variant AF is 0.0000801082

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARF2	protein_coding	protein_coding	ENST00000266214	11	13273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000202	125687	0	47	125734	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	305	494	0.618	0.0000336	5321
Missense in Polyphen		107	230.93	0.46334		2493
Synonymous	2.55	182	231	0.787	0.0000186	1787
Loss of Function	5.01	2	33.1	0.0604	0.00000158	361

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00239	0.00212
Finnish	0.00	0.00
European (Non-Finnish)	0.0000409	0.0000352
Middle Eastern	0.00239	0.00212
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable adhesion protein, which mediates homophilic and heterophilic interactions. In contrast to SCARF1, it poorly mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL) (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.145

Haploinsufficiency Scores

• pHI: 0.123
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scarf2
• Phenotype: skeleton phenotype; immune system phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
• Cellular component: focal adhesion;integral component of membrane
• Molecular function: protein binding