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12:103234241:T/G
GRCh37/hg19 position 12:103234241
GRCh38/hg38 position 12:102840463
Alleles (ref/alt) T/G
dbSNP rsid rs62644501
Gene symbol

PAH
Most severe consequence missense_variant
Flanking sequence TGGGTATTGTCCAAGACCTCAATCCTTTGGG[T/G]GTATGGGTCGTAGCGAACTGAGAAGGGCCGA
HGVS

NM_000277.3:c.1252A>C

NM_001354304.2:c.1252A>C

NP_000268.1:p.Thr418Pro

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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.1252A>C p.Thr418Pro Exon 12
NM_001354304.2 PAH 14 missense_variant c.1252A>C p.Thr418Pro 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
gnomAD exomes ALL 1 246224 0 4.06134e-06
FIN 0 22300 0 0
NFE 0 111696 0 0
ASJ 0 9850 0 0
EAS 0 17248 0 0
SAS 1 30782 0 3.24865e-05
AFR 0 15302 0 0
AMR 0 33564 0 0
OTH 0 5482 0 0
Functional predictions
Tool Score Prediction
SIFT 0 damaging
Polyphen2 HDIV 1 probably damaging
Polyphen2 HVAR 0.998 probably damaging
LRT 0.000000 deleterious
MutationTaster 1 disease_causing
MutationAssessor 4.31 high
FATHMM -6.59 damaging
MetaSVM 1.0119 damaging
MetaLR 0.991 damaging
PROVEAN -5.49 damaging
M-CAP 0.763433 damaging
CADD 4.36808 -
REVEL 0.964 -
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++ 4.17 Conserved
phastCons46way primates 0.983 Highly conserved
phastCons46way placental 0.999 Highly conserved
phastCons100way vertebrates 1.000 Highly conserved
phyloP46way primates 0.459 Not conserved
phyloP46way placental 0.965 Not conserved
phyloP100way vertebrates 5.552 Conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000088818 not provided . no assertion provided literature only not provided - - -
RCV000672448 Pathogenic 2020-06-08 reviewed by expert panel clinical testing Phenylketonuria PKU Autosomal recessive inheritance

8019568

31355225

28982351

28492532

26503515

16256386

30747360

29731766

29499199

1301187

26322415
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: Likely pathogenic
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 Thr (T) Pro (P)
Amino acid name Threonine Proline
Side chain class hydroxyl-containing cyclic
Polarity polar nonpolar
Charge (pH=7.4) neutrally charged neutrally charged
Hydropathy hydrophilic hydrophobic
Molecular weight 119.119 115.132
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).