NM_080476.5:c.1230G>T

Variant names:

• chr20-34560944-C-A
• NM_080476.5:c.1230G>T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Moderate BP6_Moderate BP7

The NM_080476.5(PIGU):​c.1230G>T​(p.Leu410Leu) variant causes a synonymous 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 Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PIGU NM_080476.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.22

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 -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BP6: Variant 20-34560944-C-A is Benign according to our data. Variant chr20-34560944-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3657835.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=1.22 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGU	NM_080476.5	c.1230G>T	p.Leu410Leu	synonymous_variant	Exon 12 of 12	ENST00000217446.8	NP_536724.1
PIGU	XM_017027664.2	c.1086G>T	p.Leu362Leu	synonymous_variant	Exon 11 of 11		XP_016883153.1
PIGU	XM_011528542.2	c.582G>T	p.Leu194Leu	synonymous_variant	Exon 6 of 6		XP_011526844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGU	ENST00000217446.8	c.1230G>T	p.Leu410Leu	synonymous_variant	Exon 12 of 12	1	NM_080476.5	ENSP00000217446.3
PIGU	ENST00000374820.6	c.1170G>T	p.Leu390Leu	synonymous_variant	Exon 11 of 11	1		ENSP00000363953.2
PIGU	ENST00000438215.1	c.468G>T	p.Leu156Leu	synonymous_variant	Exon 6 of 6	3		ENSP00000395755.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 26, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	8.2
DANN	Benign	0.85

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-33148748;