SCARB2

Chr 4AR

scavenger receptor class B member 2

Also known as: AMRF, CD36L2, EPM4, HLGP85, LGP85, LIMP-2, LIMPII, SR-BII

NCBI Gene: 950 ENSG00000138760 UniProt: Q14108 OMIM: 602257

SCARB2 encodes a type III glycoprotein located in lysosomal and endosomal limiting membranes that functions in membrane transportation and reorganization of endosomal/lysosomal compartments. Mutations cause autosomal recessive progressive myoclonic epilepsy-4 (EPM4), also known as action myoclonus-renal failure syndrome, through impaired cellular membrane transport processes.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a type III glycoprotein that is located primarily in limiting membranes of lysosomes and endosomes. Earlier studies in mice and rat suggested that this protein may participate in membrane transportation and the reorganization of endosomal/lysosomal compartment. The protein deficiency in mice was reported to impair cell membrane transport processes and cause pelvic junction obstruction, deafness, and peripheral neuropathy. Further studies in human showed that this protein is a ubiquitously expressed protein and that it is involved in the pathogenesis of HFMD (hand, foot, and mouth disease) caused by enterovirus-71 and possibly by coxsackievirus A16. Mutations in this gene caused an autosomal recessive progressive myoclonic epilepsy-4 (EPM4), also known as action myoclonus-renal failure syndrome (AMRF). Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

OMIM ResearchGenerating clinical summary…

ARLOEUF 0.721 OMIM phenotype

Clinical Summary— SCARB2

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Gene-Disease Validity (ClinGen)

progressive myoclonus epilepsy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

38 unique Pathogenic / Likely Pathogenic· 225 VUS of 559 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.72LOEUF

pLI 0.000

Z-score 2.61

OE 0.44 (0.27–0.72)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.32Z-score

OE missense 0.77 (0.68–0.86)

194 obs / 253.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.27–0.72)

0≤0.351.4

Missense OE?0.77 (0.68–0.86)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 11 / 25.1Missense obs/exp: 194 / 253.3Syn Z: 0.92

ClinVar Variant Classifications

559 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22

Likely Pathogenic16

VUS225

Likely Benign201

Benign55

Conflicting20

Pathogenic

Likely Pathogenic

225

VUS

201

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	21	0	1	0	22
Likely Pathogenic	16	0	0	0	16
VUS	3	197	22	3	225
Likely Benign	0	1	97	103	201
Benign	0	3	51	1	55
Conflicting	—				20
Total	40	201	171	107	539

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

23 pathogenic / likely-pathogenic (of 29) ClinVar copy-number / structural variants overlap SCARB2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →