rs1555683899
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_176787.5(PIGN):c.1761A>G(p.Arg587Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000689 in 1,450,500 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: not found (cov: 32)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
PIGN
NM_176787.5 synonymous
NM_176787.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.74
Publications
0 publications found
Genes affected
PIGN (HGNC:8967): (phosphatidylinositol glycan anchor biosynthesis class N) This gene encodes a protein that is involved 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 protein is expressed in the endoplasmic reticulum and transfers phosphoethanolamine (EtNP) to the first mannose of the GPI anchor. Two alternatively spliced variants, which encode an identical isoform, have been reported. [provided by RefSeq, Jul 2008]
PIGN Gene-Disease associations (from GenCC):
- multiple congenital anomalies-hypotonia-seizures syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Orphanet, ClinGen, PanelApp Australia
- Fryns syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 18-62106795-T-C is Benign according to our data. Variant chr18-62106795-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 539559.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.74 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PIGN | NM_176787.5 | c.1761A>G | p.Arg587Arg | synonymous_variant | Exon 19 of 31 | ENST00000640252.2 | NP_789744.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PIGN | ENST00000640252.2 | c.1761A>G | p.Arg587Arg | synonymous_variant | Exon 19 of 31 | 1 | NM_176787.5 | ENSP00000492233.1 | ||
| PIGN | ENST00000400334.7 | c.1761A>G | p.Arg587Arg | synonymous_variant | Exon 18 of 30 | 1 | ENSP00000383188.2 | |||
| PIGN | ENST00000638424.1 | n.1761A>G | non_coding_transcript_exon_variant | Exon 17 of 29 | 5 | ENSP00000491963.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1450500Hom.: 0 Cov.: 28 AF XY: 0.00000694 AC XY: 5AN XY: 720594 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
1450500
Hom.:
Cov.:
28
AF XY:
AC XY:
5
AN XY:
720594
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33260
American (AMR)
AF:
AC:
0
AN:
43662
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25888
East Asian (EAS)
AF:
AC:
0
AN:
39300
South Asian (SAS)
AF:
AC:
0
AN:
84172
European-Finnish (FIN)
AF:
AC:
0
AN:
52748
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
10
AN:
1105694
Other (OTH)
AF:
AC:
0
AN:
60020
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Multiple congenital anomalies-hypotonia-seizures syndrome 1 Benign:1
Apr 04, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.