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12:103232982:G/A
GRCh37/hg19 position 12:103232982
GRCh38/hg38 position 12:102839204
Alleles (ref/alt) G/A
dbSNP rsid -
Gene symbol

PAH
Most severe consequence missense_variant
Flanking sequence CTTTACTTTATTTTCTGGAGGGCACTGCAAA[G/A]GATTCCAATTTCACCTACAAAGAAAAACACC
HGVS

NM_000277.3:c.1330C>T

NM_001354304.2:c.1330C>T

NP_000268.1:p.Leu444Phe

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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.1330C>T p.Leu444Phe Exon 13
NM_001354304.2 PAH 14 missense_variant c.1330C>T p.Leu444Phe Exon 14
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 genomes ALL 1 30958 0 3.23018e-05
FIN 0 3490 0 0
NFE 1 14996 0 6.66844e-05
ASJ 0 302 0 0
EAS 0 1618 0 0
AFR 0 8732 0 0
AMR 0 838 0 0
OTH 0 982 0 0
Functional predictions
Tool Score Prediction
SIFT 0.01 damaging
Polyphen2 HDIV 0.999 probably damaging
Polyphen2 HVAR 0.99 probably damaging
LRT 0.000000 deleterious
MutationTaster 1 disease_causing
MutationAssessor 3.325 medium
FATHMM -6.58 damaging
MetaSVM 1.0081 damaging
MetaLR 0.99 damaging
PROVEAN -3.26 damaging
M-CAP 0.695257 damaging
CADD 4.387021 -
REVEL 0.885 -
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++ 5.31 Conserved
phastCons46way primates 0.976 Highly conserved
phastCons46way placental 1.000 Highly conserved
phastCons100way vertebrates 1.000 Highly conserved
phyloP46way primates 0.585 Conserved
phyloP46way placental 2.645 Conserved
phyloP100way vertebrates 5.026 Conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000666307 Conflicting interpretations of pathogenicity 2022-07-23 criteria provided, conflicting interpretations clinical testing Phenylketonuria PKU -

26600521

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 Leu (L) Phe (F)
Amino acid name Leucine Phenylalanine
Side chain class aliphatic aromatic
Polarity nonpolar nonpolar
Charge (pH=7.4) neutrally charged neutrally charged
Hydropathy hydrophobic hydrophobic
Molecular weight 131.175 165.192
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).