11-3824025-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP5BP4

The NM_014489.4(PGAP2):​c.491C>T​(p.Thr164Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

PGAP2
NM_014489.4 missense

Scores

1
18

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 3.49
Variant links:
Genes affected
PGAP2 (HGNC:17893): (post-GPI attachment to proteins 2) The protein encoded by this gene plays a role in the maturation of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins. Mutations in this gene are associated with an autosomal recessive syndrome characterized by hyperphosphatasia and intellectual disability. [provided by RefSeq, Jul 2017]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM1
In a chain Post-GPI attachment to proteins factor 2 (size 253) in uniprot entity PGAP2_HUMAN there are 16 pathogenic changes around while only 0 benign (100%) in NM_014489.4
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-3824025-C-T is Pathogenic according to our data. Variant chr11-3824025-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 50506.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.053373605). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PGAP2NM_014489.4 linkc.491C>T p.Thr164Ile missense_variant Exon 4 of 7 ENST00000278243.9 NP_055304.1 Q9UHJ9-2A0A024RCC6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PGAP2ENST00000278243.9 linkc.491C>T p.Thr164Ile missense_variant Exon 4 of 7 1 NM_014489.4 ENSP00000278243.4 Q9UHJ9-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251436
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135904
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461870
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Hyperphosphatasia with intellectual disability syndrome 3 Pathogenic:1
Apr 04, 2013
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
16
DANN
Benign
0.89
DEOGEN2
Benign
0.17
.;.;.;.;.;.;.;.;T;.
Eigen
Benign
-0.56
Eigen_PC
Benign
-0.42
FATHMM_MKL
Benign
0.30
N
LIST_S2
Uncertain
0.89
D;D;D;D;.;D;D;D;D;D
M_CAP
Benign
0.0036
T
MetaRNN
Benign
0.053
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-1.1
.;.;.;.;.;N;.;.;N;.
PrimateAI
Benign
0.40
T
PROVEAN
Benign
0.63
N;N;.;.;.;N;.;N;N;N
REVEL
Benign
0.044
Sift
Benign
0.45
T;T;.;.;.;T;.;T;T;T
Sift4G
Benign
0.47
T;T;T;T;T;T;T;T;T;T
Polyphen
0.55
P;.;.;.;.;.;.;.;.;.
Vest4
0.31
MutPred
0.35
Gain of helix (P = 0.1736);Gain of helix (P = 0.1736);.;.;.;.;.;.;.;.;
MVP
0.28
MPC
0.40
ClinPred
0.23
T
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.048
gMVP
0.20

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587776970; hg19: chr11-3845255; API