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12:103234229:C/T
GRCh37/hg19 position 12:103234229
GRCh38/hg38 position 12:102840451
Alleles (ref/alt) C/T
dbSNP rsid rs199475621
Gene symbol

PAH
Most severe consequence missense_variant
Flanking sequence ATCTTAAGCTGCTGGGTATTGTCCAAGACCT[C/T]AATCCTTTGGGTGTATGGGTCGTAGCGAACT
HGVS

NM_000277.3:c.1264G>A

NM_001354304.2:c.1264G>A

NP_000268.1:p.Glu422Lys

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Gene annotations
Transcript Gene Exon number Consequence HGVS cDNA HGVS protein Location Protein location
NM_000277.3 PAH 13 missense_variant c.1264G>A p.Glu422Lys Exon 12
NM_001354304.2 PAH 14 missense_variant c.1264G>A p.Glu422Lys Exon 13
Population frequency
Select populations: ALL LWK MKK YRI EUR FIN NFE CEU ASJ TSI EAS SAS CHB HAN CHD JPT AFR AMR ASW GIH MEX OTH
Database Population AC AN Hom AF
Functional predictions
Tool Score Prediction
SIFT 0.002 damaging
Polyphen2 HDIV 0.989 probably damaging
Polyphen2 HVAR 0.905 possibly damaging
LRT 0.000000 deleterious
MutationTaster 1 disease_causing
MutationAssessor 3.04 medium
FATHMM -6.3 damaging
MetaSVM 1.0375 damaging
MetaLR 0.9863 damaging
PROVEAN -3.28 damaging
M-CAP 0.713738 damaging
CADD 4.45801 -
REVEL 0.96 -
Conservation
Conservation scores are retrieved from UCSC genome browser. The conservation levels are defined by simple cutoff values. If the conservation levels do not agree with each other, you can manually check whether this variant is conserved with UCSC genome browser.
Method Score Level
GERP++ 5.33 Conserved
phastCons46way primates 0.997 Highly conserved
phastCons46way placental 1.000 Highly conserved
phastCons100way vertebrates 1.000 Highly conserved
phyloP46way primates 0.561 Conserved
phyloP46way placental 2.664 Conserved
phyloP100way vertebrates 7.049 Conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000088821 not provided . no assertion provided literature only not provided - - -
RCV001199987 Uncertain significance 2020-03-27 reviewed by expert panel curation Phenylketonuria PKU Autosomal recessive inheritance

10541324

31737040

28492532
InterVar

InterVar is a software tool for clinical interpretation of genetic variants by the ACMG/AMP 2015 guideline. The eveidence tags that variant met are highlighted. Please note that evidence tags with need to be evaluated manually.

Class: Uncertain significance
Benign Pathogenic
Strong Supporting Supporting Moderate Strong Very Strong
Population data BA1
BS1
BS2 		PM2 PS4
Computational and predictive data BP1
BP3
BP4
BP7 		PP3 PM4
PM5		 PS1 PVS1
Functional data BS3 PP2 PM1 PS3
Segregation data BS4 PP1 PP1 PP1
De novo data PM6 PS2
Allelic data BP2 PM3
Other database BP6 PP5
Other data BP5 PP4
Amino acid change

The physichemical property of amino acid change.

Trait Glu (E) Lys (K)
Amino acid name Glutamic acid Lysine
Side chain class acid basic
Polarity acidic polar basic polar
Charge (pH=7.4) negatively charged positively chared
Hydropathy hydrophilic hydrophilic
Molecular weight 147.131 146.189
gnomAD
The Genome Aggregation Database (gnomAD), is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. In its first release, which contained exclusively exome data, it was known as the Exome Aggregation Consortium (ExAC).