rs587777658

Variant names:

• chr22-20425444-CT-C
• rs587777658
• NM_182895.5:c.2531delA

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP5

The NM_182895.5(SCARF2):​c.2531delA​(p.Gln844ArgfsTer95) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SCARF2 NM_182895.5 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.03
• Publications: 1 publications found

Genes affected

SCARF2 (HGNC:19869): (scavenger receptor class F member 2) The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

SCARF2 Gene-Disease associations (from GenCC):

• van den Ende-Gupta syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ENSG00000305663 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 22-20425444-CT-C is Pathogenic according to our data. Variant chr22-20425444-CT-C is described in ClinVar as Pathogenic. ClinVar VariationId is 144051.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARF2	NM_182895.5	c.2531delA	p.Gln844ArgfsTer95	frameshift_variant	Exon 11 of 11	ENST00000622235.5	NP_878315.2
SCARF2	NM_153334.7	c.2546delA	p.Gln849ArgfsTer95	frameshift_variant	Exon 11 of 11		NP_699165.3
SCARF2	XM_047441585.1	c.2645delA	p.Gln882ArgfsTer95	frameshift_variant	Exon 11 of 11		XP_047297541.1
SCARF2	XM_017029065.3	c.*760delA		3_prime_UTR_variant	Exon 11 of 11		XP_016884554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARF2	ENST00000622235.5	c.2531delA	p.Gln844ArgfsTer95	frameshift_variant	Exon 11 of 11	1	NM_182895.5	ENSP00000477564.2
SCARF2	ENST00000623402.1	c.2546delA	p.Gln849ArgfsTer95	frameshift_variant	Exon 11 of 11	1		ENSP00000485276.1
ENSG00000305663	ENST00000812275.1	n.32+64delT		intron_variant	Intron 1 of 1
ENSG00000305663	ENST00000812276.1	n.35+64delT		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Van den Ende-Gupta syndrome Pathogenic:1

May 01, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0
Mutation Taster		=1/199	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587777658; hg19: chr22-20779734;