7-16091697-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001101426.4(CRPPA):c.1354T>A(p.Ter452ArgextTer28) variant causes a stop lost change. The variant allele was found at a frequency of 0.00000458 in 1,527,814 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000036 ( 0 hom. )
Consequence
CRPPA
NM_001101426.4 stop_lost
NM_001101426.4 stop_lost
Scores
2
1
4
Clinical Significance
Conservation
PhyloP100: 3.76
Genes affected
CRPPA (HGNC:37276): (CDP-L-ribitol pyrophosphorylase A) This gene encodes a 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase-like protein. Mutations in this gene are the cause of Walker-Warburg syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_addAF=-0.143947).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRPPA | NM_001101426.4 | c.1354T>A | p.Ter452ArgextTer28 | stop_lost | 10/10 | ENST00000407010.7 | |
CRPPA | NM_001368197.1 | c.1249T>A | p.Ter417ArgextTer28 | stop_lost | 9/9 | ||
CRPPA | NM_001101417.4 | c.1204T>A | p.Ter402ArgextTer28 | stop_lost | 9/9 | ||
CRPPA | NR_160656.1 | n.1419T>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRPPA | ENST00000407010.7 | c.1354T>A | p.Ter452ArgextTer28 | stop_lost | 10/10 | 5 | NM_001101426.4 | P1 | |
CRPPA | ENST00000399310.3 | c.1204T>A | p.Ter402ArgextTer28 | stop_lost | 9/9 | 1 | |||
CRPPA | ENST00000676325.1 | c.1051T>A | p.Ter351ArgextTer28 | stop_lost | 11/11 | ||||
CRPPA | ENST00000675257.1 | c.946T>A | p.Ter316ArgextTer28 | stop_lost | 10/10 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000252 AC: 4AN: 158570Hom.: 0 AF XY: 0.0000239 AC XY: 2AN XY: 83784
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GnomAD4 exome AF: 0.00000364 AC: 5AN: 1375500Hom.: 0 Cov.: 24 AF XY: 0.00000441 AC XY: 3AN XY: 680340
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74464
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7 Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Daryl Scott Lab, Baylor College of Medicine | Nov 10, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 01, 2017 | This mutation has been previously reported as disease-causing and was found once in our laboratory in trans with a nonsense mutation in a newborn female with MRI suggestive of Walker-Warburg, microphthalmia, possible cataract, encephalocele, hypotonia, dysmorhisms - |
Autosomal recessive limb-girdle muscular dystrophy type 2U Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | 3billion | Feb 23, 2023 | The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.003%). Predicted Consequence/Location: Stop lost variant. The variant has been reported to be associated with CRPPA related disorder (PMID: 22522420, ClinVar ID: VCV000561034.2). However, the evidence of pathogenicity is insufficient at this time. Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline. - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7;C5190987:Autosomal recessive limb-girdle muscular dystrophy type 2U Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2022 | This sequence change disrupts the translational stop signal of the ISPD mRNA. It is expected to extend the length of the ISPD protein by 28 additional amino acid residues. This variant is present in population databases (rs186882839, gnomAD 0.02%). This protein extension has been observed in individual(s) with Walker-Warburg syndrome (PMID: 22522420, 28973083). ClinVar contains an entry for this variant (Variation ID: 561034). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
N;N
Vest4
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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