SOAT1 p.Leu475Leu

Variant names:

• chr1-179350403-G-G
• ENST00000367619.8:c.

Your query was ambiguous. Multiple possible variants found:

• chr1-179350404--
• chr1-179350406-C-T
• chr1-179350406-C-A
• chr1-179350406-C-G
• chr1-179350404-CTC-TTA
• chr1-179350404-CTC-TTG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_003101.6(SOAT1):​c. variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SOAT1 NM_003101.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.95
• Publications: 0 publications found

Genes affected

SOAT1 (HGNC:11177): (sterol O-acyltransferase 1) The protein encoded by this gene belongs to the acyltransferase family. It is located in the endoplasmic reticulum, and catalyzes the formation of fatty acid-cholesterol esters. This gene has been implicated in the formation of beta-amyloid and atherosclerotic plaques by controlling the equilibrium between free cholesterol and cytoplasmic cholesteryl esters. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003101.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOAT1	NM_003101.6	MANE Select	c.		intron	N/A	NP_003092.4
	SOAT1	NM_001252511.2		c.		intron	N/A	NP_001239440.1	P35610-2
	SOAT1	NM_001252512.2		c.		intron	N/A	NP_001239441.1	P35610-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOAT1	ENST00000367619.8	TSL:1 MANE Select	c.		exon_region	Exon 14 of 16	ENSP00000356591.3	P35610-1
	SOAT1	ENST00000540564.5	TSL:1	c.		exon_region	Exon 13 of 15	ENSP00000445315.1	P35610-2
	SOAT1	ENST00000904814.1		c.		exon_region	Exon 14 of 16	ENSP00000574873.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-179319538;