2-196841061-T-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024989.4(PGAP1):c.*173A>G variant causes a 3 prime UTR 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PGAP1
NM_024989.4 3_prime_UTR
NM_024989.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.313
Publications
0 publications found
Genes affected
PGAP1 (HGNC:25712): (post-GPI attachment to proteins inositol deacylase 1) The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause an autosomal recessive form of cognitive impairment. [provided by RefSeq, Jul 2017]
PGAP1 Gene-Disease associations (from GenCC):
- intellectual disability, autosomal recessive 42Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- autosomal recessive non-syndromic intellectual disabilityInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal recessive spastic paraplegia type 67Inheritance: 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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024989.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PGAP1 | TSL:1 MANE Select | c.*173A>G | 3_prime_UTR | Exon 27 of 27 | ENSP00000346809.3 | Q75T13-1 | |||
| PGAP1 | TSL:1 | n.*2873A>G | non_coding_transcript_exon | Exon 28 of 28 | ENSP00000415405.1 | F8WD75 | |||
| PGAP1 | TSL:1 | n.*2873A>G | 3_prime_UTR | Exon 28 of 28 | ENSP00000415405.1 | F8WD75 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 589090Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 302050
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
589090
Hom.:
Cov.:
8
AF XY:
AC XY:
0
AN XY:
302050
African (AFR)
AF:
AC:
0
AN:
15148
American (AMR)
AF:
AC:
0
AN:
16660
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13760
East Asian (EAS)
AF:
AC:
0
AN:
32106
South Asian (SAS)
AF:
AC:
0
AN:
37722
European-Finnish (FIN)
AF:
AC:
0
AN:
39326
Middle Eastern (MID)
AF:
AC:
0
AN:
2344
European-Non Finnish (NFE)
AF:
AC:
0
AN:
402350
Other (OTH)
AF:
AC:
0
AN:
29674
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
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.