12-102894893-A-G

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PM1PM5PP2PP3_ModeratePP5_Very_Strong

The NM_000277.3(PAH):​c.194T>C​(p.Ile65Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0006 in 1,613,738 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I65N) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.00030 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 1 hom. )

Consequence

PAH
NM_000277.3 missense

Scores

16
2

Clinical Significance

Pathogenic reviewed by expert panel P:27O:2

Conservation

PhyloP100: 8.30

Publications

103 publications found
Variant links:
Genes affected
PAH (HGNC:8582): (phenylalanine hydroxylase) This gene encodes a member of the biopterin-dependent aromatic amino acid hydroxylase protein family. The encoded phenylalanine hydroxylase enzyme hydroxylates phenylalanine to tyrosine and is the rate-limiting step in phenylalanine catabolism. Deficiency of this enzyme activity results in the autosomal recessive disorder phenylketonuria. [provided by RefSeq, Aug 2017]
PAH Gene-Disease associations (from GenCC):
  • phenylketonuria
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Myriad Women’s Health
  • classic phenylketonuria
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • maternal phenylketonuria
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • mild hyperphenylalaninemia
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • mild phenylketonuria
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • tetrahydrobiopterin-responsive hyperphenylalaninemia/phenylketonuria
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 15 ACMG points.

PM1
In a hotspot region, there are 18 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 10 uncertain in NM_000277.3
PM5
Other missense variant is known to change same aminoacid residue: Variant chr12-102894893-A-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 102623.Status of the report is reviewed_by_expert_panel, 3 stars.
PP2
Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 440 curated pathogenic missense variants (we use a threshold of 10). The gene has 8 curated benign missense variants. Gene score misZ: -0.64755 (below the threshold of 3.09). Trascript score misZ: -0.0084567 (below the threshold of 3.09). GenCC associations: The gene is linked to phenylketonuria, tetrahydrobiopterin-responsive hyperphenylalaninemia/phenylketonuria, maternal phenylketonuria, classic phenylketonuria, mild phenylketonuria, mild hyperphenylalaninemia.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.93
PP5
Variant 12-102894893-A-G is Pathogenic according to our data. Variant chr12-102894893-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 636.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PAHNM_000277.3 linkc.194T>C p.Ile65Thr missense_variant Exon 3 of 13 ENST00000553106.6 NP_000268.1
PAHNM_001354304.2 linkc.194T>C p.Ile65Thr missense_variant Exon 4 of 14 NP_001341233.1
PAHXM_017019370.2 linkc.194T>C p.Ile65Thr missense_variant Exon 3 of 7 XP_016874859.1
LOC124902999XR_007063428.1 linkn.863-9805A>G intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PAHENST00000553106.6 linkc.194T>C p.Ile65Thr missense_variant Exon 3 of 13 1 NM_000277.3 ENSP00000448059.1

Frequencies

GnomAD3 genomes
AF:
0.000296
AC:
45
AN:
152226
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000529
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.000271
AC:
68
AN:
251202
AF XY:
0.000265
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.0000867
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000537
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000632
AC:
924
AN:
1461512
Hom.:
1
Cov.:
30
AF XY:
0.000633
AC XY:
460
AN XY:
727086
show subpopulations
African (AFR)
AF:
0.000119
AC:
4
AN:
33478
American (AMR)
AF:
0.0000894
AC:
4
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26132
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39690
South Asian (SAS)
AF:
0.0000348
AC:
3
AN:
86258
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53304
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
0.000789
AC:
877
AN:
1111782
Other (OTH)
AF:
0.000596
AC:
36
AN:
60378
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.453
Heterozygous variant carriers
0
42
84
126
168
210
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
40
80
120
160
200
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000296
AC:
45
AN:
152226
Hom.:
0
Cov.:
32
AF XY:
0.000309
AC XY:
23
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.000169
AC:
7
AN:
41458
American (AMR)
AF:
0.000131
AC:
2
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5204
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4834
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10614
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.000529
AC:
36
AN:
68044
Other (OTH)
AF:
0.00
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
3
6
9
12
15
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000481
Hom.:
0
Bravo
AF:
0.000302
TwinsUK
AF:
0.00108
AC:
4
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000581
AC:
5
ExAC
AF:
0.000181
AC:
22
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000436
EpiControl
AF:
0.000474

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:27Other:2
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Phenylketonuria Pathogenic:16Other:1
Sep 16, 2020
Natera, Inc.
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

Apr 28, 2022
Fulgent Genetics, Fulgent Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Dec 30, 2024
3billion
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.060%). Predicted Consequence/Location: Missense variant Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 1301201). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.98 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.99 (>=0.6, sensitivity 0.72 and precision 0.9)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000000636 /PMID: 1301187 /3billion dataset). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 10767174, 12501224, 1301201). Different missense changes at the same codon (p.Ile65Asn, p.Ile65Ser, p.Ile65Val) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000102622, VCV000102623 /PMID: 12501224, 22526846, 9521426). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

Jul 19, 2016
Division of Human Genetics, Children's Hospital of Philadelphia
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:research

Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 65 of the PAH protein (p.Ile65Thr). This variant is present in population databases (rs75193786, gnomAD 0.05%). This missense change has been observed in individual(s) with PAH-related conditions (PMID: 12655546, 23500595, 25596310). ClinVar contains an entry for this variant (Variation ID: 636). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt PAH protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PAH function (PMID: 12655546, 17935162, 26803807). For these reasons, this variant has been classified as Pathogenic.

Jan 26, 2017
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Variant summary: The PAH c.194T>C (p.Ile65Thr) variant located in the ACT domain (via InterPro) involves the alteration of a conserved nucleotide, which 5/5 in silico tools predict a damaging outcome. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 22/121240 (1/5509), which does not exceed the estimated maximal expected allele frequency for a pathogenic PAH variant of 1/126. Multiple publications cite the variant in affected individuals, predominantly as compound heterozygous and was indicated to cause a mild PKU phenotype. In addition, multiple clinical diagnostic laboratories and databases cite the variant as "pathogenic." Therefore, the variant of interest has been classified as "Pathogenic."

Jun 29, 2022
Revvity Omics, Revvity
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Dec 24, 2019
Myriad Genetics, Inc.
Significance:Likely pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

NM_000277.1(PAH):c.194T>C(I65T) is classified as likely pathogenic in the context of phenylalanine hydroxylase deficiency and may be associated with classic, variant, or non-PKU hyperphenylalaninemia. Sources cited for classification include the following: PMID 11524738, 23500595, 11326337, 1301187, 17935162, 15557004, 8533759, and 9781015. Classification of NM_000277.1(PAH):c.194T>C(I65T) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

GeneReviews
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:research

The PAH c.194T>C (p.I65T) missense variant has been found in the homozygous and compound heterozygous state in individuals with a range of clinical phenotypes including hyperphenylalaninemia; mild phenylketonuria, and classic phenylketonuria (PMID: 9254847; 1301201; 10767174; 12501224).

Jul 26, 2022
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

PS3, PM3_Very Strong, PP3

Mar 30, 2024
Baylor Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Apr 08, 2023
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:research

Apr 21, 2018
ClinGen PAH Variant Curation Expert Panel
Significance:Pathogenic
Review Status:reviewed by expert panel
Collection Method:curation

PAH-specific ACMG/AMP criteria applied: PM3_VeryStrong: Detected with Y414C (P), R408W (P), P281L (P), IVS10nt-11 (P), R252W (P/LP), and R243Q(P). (PMID:12501224; PMID:1301201; PMID:10767174); PP3: Predicted dleterious in SIZFT, Polyphen2, MutationTaster. REVEL=0.985; PP4_Moderate: Detected in a patient with mild PKU. BH4 deficiency excluded. Upgraded per ClinGen PAH EP. (PMID:12501224); PS3: 25% mutant enzyme activity in COS cells as compared in wt (PMID:1301201). In summary this variant meets criteria to be classified as pathogenic for phenylketonuria in an autosomal recessive manner based on the ACMG/AMP criteria applied as specified by the PAH Expert Panel: (PM3_VeryStrong, PP3, PP4_Moderate, PS3).

Juno Genomics, Hangzhou Juno Genomics, Inc
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

For recessive disorders, detected in trans with a pathogenic variant.;Patient's phenotype or family history is highly specific for a disease with a single genetic etiology.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Aug 22, 2025
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is classified as Pathogenic. Evidence in support of pathogenic classification: Variant is present in gnomAD <0.01 for a recessive condition (v4: 967 heterozygote(s), 1 homozygote(s)); This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by the ClinGen PAH Variant Curation Expert Panel (ClinVar). It is one of the most common pathogenic variants reported in individuals with classic PKU (PMID: 33465300, BIOPKU database). Additional information: Variant is predicted to result in a missense amino acid change from Ile to Thr; This variant is heterozygous; This gene is associated with autosomal recessive disease; Variant is located in the annotated ACT domain (DECIPHER); Loss of function is a known mechanism of disease in this gene and is associated with phenylketonuria (MIM#261600).

Jan 01, 1992
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only

not provided Pathogenic:8Other:1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Significance:Likely pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

DeBelle Laboratory for Biochemical Genetics, MUHC/MCH RESEARCH INSTITUTE
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

Sep 22, 2020
GeneDx
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Common pathogenic PAH variant most often reported in association with mild-moderate phenylketonuria (PKU) (Pey et al., 2007; Zurfluh et al, 2008; Danecka et al. 2015). It has also been identified in an individual with classic PKU (Couce et al., 2013).; Functional studies demonstrate I65T is associated with reduced phenylalanine hydroxylase activity compared to wild-type (Danecka et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 1301187, 17924342, 1301201, 22975760, 30963030, 23500595, 17935162, 11326337, 23559577, 12655546, 25596310, 19036622, 11461190, 21953985, 27121329, 28645531, 25087612, 27264808, 26803807, 19194782, 29030855, 30648773, 30747360, 31980526, 30275481, 31589614, 32668217, 32853555)

Jul 02, 2018
Eurofins Ntd Llc (ga)
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

Apr 27, 2021
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The PAH c.194T>C (p.Ile65Thr) variant is associated with a variable phenotype that ranges from non-PKU hyperphenylalaninemia to classic PKU (PMID: 1301201 (1992), 12501224 (2002), 15557004 (2004)). Assessment of experimental evidence regarding the effect of this variant suggests it causes decreased enzyme activity with a residual activity of about 30% (PMID: 26803807 (2016), 12655546 (2003), 1301201 (1992)). Therefore, the variant is classified as pathogenic.

Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

Sep 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

PAH: PM3:Very Strong, PM2, PM5, PP4:Moderate, PP3, PS3:Supporting

May 29, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

PP3, PP4_moderate, PM2_moderate, PM3_very_strong

PAH-related disorder Pathogenic:1
May 02, 2024
PreventionGenetics, part of Exact Sciences
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:clinical testing

The PAH c.194T>C variant is predicted to result in the amino acid substitution p.Ile65Thr. This variant has been reported in the literature as causative for phenylalanine hydroxylase deficiency (for example, see Eisensmith and Woo et al. 1992. PubMed ID: 1301187; Zschocke et al. 1995. PubMed ID: 8533759; Jeannesson-Thivisol et al. 2015. PubMed ID: 26666653; Hillert et al. 2020. PubMed ID: 32668217; Vela-Amieva et al. 2021. PubMed ID: 34828281). Based on functional studies, the p.Ile65Thr amino acid change has been reported to result in reduced PAH protein level and reduced enzyme activity, and has been classified as a BH4-responsive amino acid substitution (Zurflüh et al. 2008. PubMed ID: 17935162; Shi et al. 2012. PubMed ID: 21953985). Multiple other laboratories, as well as the ClinGen PAH Variant Curation Expert Panel, classify this variant as pathogenic or likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/636/). Based on these observations, this variant is interpreted as pathogenic.

Inborn genetic diseases Pathogenic:1
Dec 23, 2024
Ambry Genetics
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.194T>C (p.I65T) alteration is located in coding exon 3 of the PAH gene. This alteration results from a T to C substitution at nucleotide position 194, causing the isoleucine (I) at amino acid position 65 to be replaced by a threonine (T). Based on data from the Genome Aggregation Database (gnomAD), the PAH c.194T>C alteration was observed in 0.03% (83/282610) of total alleles studied, with a frequency of 0.06% (72/129008) in the European (non-Finnish) subpopulation. No homozygotes were observed. The c.194T>C (p.I65T) alteration has been described homozygous and compound heterozygous with a second allele in multiple unrelated families with phenotypes ranging from hyperphenylalaninemia to classic PKU (Couce, 2013; Desviat, 2004; John, 1992; Muntau, 2002; Rivera, 2000). The p.I65 amino acid is conserved in available vertebrate species. In vitro functional studies determined protein expressing the c.194T>C (p.I65T) alteration decreased PAH activity to less than 50% of wild type activity. When observed with a second deleterious alteration, residual PAH activity ranged between 5.5% to 48% (John, 1992; Shen, 2016). The p.I65T alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

See cases Pathogenic:1
Mar 08, 2019
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Significance:Pathogenic
Review Status:criteria provided, single submitter
Collection Method:clinical testing

ACMG classification criteria: PS3, PS4, PM1, PM2, PM3, PP3

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.95
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.59
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.99
D;D;D;D
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
1.0
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.99
D;D;D;D
M_CAP
Pathogenic
0.87
D
MetaRNN
Pathogenic
0.93
D;D;D;D
MetaSVM
Pathogenic
0.98
D
MutationAssessor
Pathogenic
4.3
H;.;.;.
PhyloP100
8.3
PrimateAI
Uncertain
0.76
T
PROVEAN
Pathogenic
-4.5
D;D;D;D
REVEL
Pathogenic
0.98
Sift
Pathogenic
0.0
D;D;D;D
Sift4G
Pathogenic
0.0010
D;D;D;.
Vest4
0.95
ClinPred
0.94
D
GERP RS
6.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.99
gMVP
0.92
Mutation Taster
=1/99
disease causing (ClinVar)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs75193786; hg19: chr12-103288671; API