20-34562555-C-T

Variant names:

• chr20-34562555-C-T
• rs1199130637
• NM_080476.5:c.1195-1576G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_080476.5(PIGU):​c.1195-1576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PIGU NM_080476.5 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.498

Genes affected

PIGU (HGNC:15791): (phosphatidylinositol glycan anchor biosynthesis class U) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Cdc91, a predicted integral membrane protein that may function in cell division control. The protein encoded by this gene is the fifth subunit of GPI transamidase that attaches GPI-anchors to proteins. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGU	NM_080476.5	c.1195-1576G>A		intron_variant	Intron 11 of 11	ENST00000217446.8	NP_536724.1
PIGU	XM_017027664.2	c.1051-1576G>A		intron_variant	Intron 10 of 10		XP_016883153.1
PIGU	XM_011528542.2	c.547-1576G>A		intron_variant	Intron 5 of 5		XP_011526844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGU	ENST00000217446.8	c.1195-1576G>A		intron_variant	Intron 11 of 11	1	NM_080476.5	ENSP00000217446.3
PIGU	ENST00000374820.6	c.1135-1576G>A		intron_variant	Intron 10 of 10	1		ENSP00000363953.2
PIGU	ENST00000438215.1	c.433-1576G>A		intron_variant	Intron 5 of 5	3		ENSP00000395755.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Glycosylphosphatidylinositol biosynthesis defect 21 Uncertain:1

Aug 06, 2019

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The PIGU c.1195-1576G>A variant is an intronic variant. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is not found in the Genome Aggregation Database (version 2.1.1). Based on the limited evidence, the c.1195-1576G>A variant is classified as a variant of uncertain significance for glycosylphosphatidylinositol biosynthesis defect. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1199130637; hg19: chr20-33150359;