chr16-574503-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1

The NM_004204.5(PIGQ):c.429G>A(p.Leu143Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000197 in 1,607,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 34)

Exomes 𝑓: 0.00020 ( 0 hom. )

Consequence

PIGQ
NM_004204.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -3.27

Publications

1 publications found

Variant links:

Genes affected

PIGQ (HGNC:14135): (phosphatidylinositol glycan anchor biosynthesis class Q) This gene is involved in the first step in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This gene encodes a N-acetylglucosaminyl transferase component that is part of the complex that catalyzes transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

PIGQ Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy, 77
Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
genetic developmental and epileptic encephalopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

PIGQ links:

ENSG00000282907 (HGNC:):

ENSG00000282907 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 16-574503-G-A is Benign according to our data. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-574503-G-A is described in CliVar as Likely_benign. Clinvar id is 526285.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.000201 (293/1455314) while in subpopulation MID AF = 0.00264 (15/5688). AF 95% confidence interval is 0.00162. There are 0 homozygotes in GnomAdExome4. There are 152 alleles in the male GnomAdExome4 subpopulation. Median coverage is 40. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGQ	NM_004204.5 link	c.429G>A	p.Leu143Leu	synonymous_variant	Exon 2 of 11	ENST00000321878.10	NP_004195.2	Q9BRB3-2B2RAU6
PIGQ	NM_148920.4 link	c.429G>A	p.Leu143Leu	synonymous_variant	Exon 2 of 10		NP_683721.1	Q9BRB3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGQ	ENST00000321878.10 link	c.429G>A	p.Leu143Leu	synonymous_variant	Exon 2 of 11	1	NM_004204.5	ENSP00000326674.6		Q9BRB3-2

Frequencies

GnomAD3 genomes

AF:

0.000151

AC:

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000206

Gnomad OTH

AF:

0.000478

GnomAD2 exomes

AF:

0.000258

AC:

AN:

232620

AF XY:

0.000243

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000179

Gnomad ASJ exome

AF:

0.000727

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000510

Gnomad NFE exome

AF:

0.000378

Gnomad OTH exome

AF:

0.000876

GnomAD4 exome

AF:

0.000201

AC:

293

AN:

1455314

Hom.:

Cov.:

AF XY:

0.000210

AC XY:

152

AN XY:

723536

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33406

American (AMR)

AF:

0.000158

AC:

AN:

44236

Ashkenazi Jewish (ASJ)

AF:

0.000808

AC:

AN:

25984

East Asian (EAS)

AF:

0.00

AC:

AN:

39492

South Asian (SAS)

AF:

0.0000469

AC:

AN:

85342

European-Finnish (FIN)

AF:

0.0000195

AC:

AN:

51166

Middle Eastern (MID)

AF:

0.00264

AC:

AN:

5688

European-Non Finnish (NFE)

AF:

0.000206

AC:

229

AN:

1109904

Other (OTH)

AF:

0.000266

AC:

AN:

60096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000151

AC:

AN:

152306

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0000481

AC:

AN:

41568

American (AMR)

AF:

0.0000654

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.000207

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000206

AC:

AN:

68008

Other (OTH)

AF:

0.000473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000282

Hom.:

Bravo

AF:

0.000215

ClinVar

Significance: Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

PIGQ: BP4, BP7 -

PIGQ-related disorder

Benign:1

Feb 28, 2024

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Epilepsy

Benign:1

Nov 27, 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

-0.85

CADD

Benign

0.0070

(source)

DANN

Benign

0.52

PhyloP100

-3.3

Mutation Taster

=100/0

polymorphism

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over