chr2-46612316-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_002643.4(PIGF):c.349G>T(p.Val117Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000275 in 1,455,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
PIGF
NM_002643.4 missense
NM_002643.4 missense
Scores
3
6
10
Clinical Significance
Conservation
PhyloP100: 4.22
Genes affected
PIGF (HGNC:8962): (phosphatidylinositol glycan anchor biosynthesis class F) This gene encodes a protein involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor, a glycolipid containing three mannose molecules in its core backbone, is found on many blood cells where it serves to anchor proteins to the cell surface. The encoded protein and another GPI synthesis protein, PIGO, function in the transfer of ethanolaminephosphate to the third mannose in GPI. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.786
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGF | NM_002643.4 | c.349G>T | p.Val117Phe | missense_variant | 4/6 | ENST00000281382.11 | NP_002634.1 | |
PIGF | NM_173074.3 | c.349G>T | p.Val117Phe | missense_variant | 4/7 | NP_775097.1 | ||
PIGF | XM_011532908.4 | c.349G>T | p.Val117Phe | missense_variant | 4/7 | XP_011531210.1 | ||
PIGF | XM_005264369.4 | c.349G>T | p.Val117Phe | missense_variant | 4/6 | XP_005264426.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGF | ENST00000281382.11 | c.349G>T | p.Val117Phe | missense_variant | 4/6 | 1 | NM_002643.4 | ENSP00000281382 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150862Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000153 AC: 2AN: 1304996Hom.: 0 Cov.: 21 AF XY: 0.00000155 AC XY: 1AN XY: 647230
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GnomAD4 genome AF: 0.0000133 AC: 2AN: 150862Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73612
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 10, 2023 | The c.349G>T (p.V117F) alteration is located in exon 4 (coding exon 3) of the PIGF gene. This alteration results from a G to T substitution at nucleotide position 349, causing the valine (V) at amino acid position 117 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MutPred
Loss of stability (P = 0.0506);Loss of stability (P = 0.0506);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at