owencqueen/cgbench_data huggingface dataset:
Gene: PAH (HGNC:8582)
Evidence Code: PVS1 — Very Strong
Modification Type: Disease-specific
Applicable as described in Tayoun et al. 2018.




Any nonsense or frameshift variant occurring upstream of c.1285


Any canonical splice site predicted to disrupt reading frame and undergo nonsense mediated decay




PVS1 (RNA): splicing assay data - assays demonstrating a variant leads to aberrant splicing profile that can be categorized against a PVS1 decision tree




Use the PVS1 decision tree to determine code strength


Applicable as described in Walker et al. (PMID: 36865205)
Gene: PAH (HGNC:8582)
Evidence Code: PVS1 — Strong
Modification Type: Disease-specific
Use PVS1_strong with:




Any nonsense or frameshift variant occurring downstream of c.1285


Any canonical splice site predicted to preserve reading frame (skipping of exons 1, 9, 10) or affect the last exon (exon 13)


Initiator codon variant
Gene: PAH (HGNC:8582)
Evidence Code: PS1 — Strong
Modification Type: Disease-specific
Same predicted splicing impact as a previously classified (likely) pathogenic variant


Applicable as described in Walker et al. (PMID: 36865205)
Gene: PAH (HGNC:8582)
Evidence Code: PS2 — Strong
Modification Type: Disease-specific
Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity. Only applicable when proband has a known pathogenic variant in trans with the de novo variant.
Gene: PAH (HGNC:8582)
Evidence Code: PS3 — Moderate
Modification Type: Disease-specific
Functional studies with sufficient analyses to calculate OddsPath reaching strong have not been identified. Therefore, the strength of this criteria is modified to PS3_moderate or PS3_supporting for future or existing studies.


In vitro enzyme activity <50% compared to wild type controls.




Expression systems placing the mutant (and wild-type) cDNAs into plasmid vectors and introducing these into human or other mammalian host cells, which is the closest available approximation to the in vivo situation (e.g., COS cells) (Trunzo et al. Gene. 2016. 594:138-143. PMID: 27620137).


With ≥11 benign/pathogenic variant controls used in assay


NOTE: no papers that meet PS3_Moderate criteria have been identified by the PAH VCEP at time of this specification update. However, there may be future studies that meet the above criteria where a moderate level of evidence can be applied.
Gene: PAH (HGNC:8582)
Evidence Code: PS3 — Supporting
Modification Type: Strength
In vitro enzyme activity ≤50% compared to wild type controls




with ≤10 benign/pathogenic variant controls used in assay
Gene: PAH (HGNC:8582)
Evidence Code: PM1 — Moderate
Modification Type: Gene-specific
Active site residues in PAH include: Tyr138, Arg158, Val245, Tyr268, Thr278, Pro279, Glu289, Ala300, Asp315, Phe331, Ala345, Gly346, Ser349, Tyr377


Substrate binding residues in PAH are: 46-48, 63-69


Cofactor binding residues in PAH are: His285, His290, Glu330, 246-266, 280-283, 322-326, 377-379


Do not apply if PP3_Strong applies
Gene: PAH (HGNC:8582)
Evidence Code: PM2 — Supporting
Modification Type: Strength
Threshold <0.0002 (0.02%)




The 0.0002 cutoff is based on disease frequency of 1:12,000 and the most common PAH pathogenic variant, R408W, the ExAC frequency is 0.0006594 (ExAC MAF: 0.001109 74/66718 European Non-Finnish) and gnomAD overall: 0.0009056 (gnomAD MAF: 0.001728 219/126,700 European Non-Finnish).
Gene: PAH (HGNC:8582)
Evidence Code: PM3 — Very Strong
Modification Type: Strength
Applicable as described in SVI recommendations for in trans criterion
Gene: PAH (HGNC:8582)
Evidence Code: PM3 — Strong
Modification Type: Strength
Applicable as described in SVI recommendations for in trans criterion
Gene: PAH (HGNC:8582)
Evidence Code: PM3 — Moderate
Modification Type: Strength
Applicable as described in SVI recommendations for in trans criterion
Gene: PAH (HGNC:8582)
Evidence Code: PM3 — Supporting
Modification Type: Strength
Applicable as described in SVI recommendations for in trans criterion
Gene: PAH (HGNC:8582)
Evidence Code: PM4 — Moderate
Modification Type: No change
Applicable as described
Gene: PAH (HGNC:8582)
Evidence Code: PM5 — Moderate
Modification Type: No change
Applicable as described.
Gene: PAH (HGNC:8582)
Evidence Code: PM5 — Supporting
Modification Type: Strength
Applicable when the different missense change is likely pathogenic.
Gene: PAH (HGNC:8582)
Evidence Code: PP1 — Strong
Modification Type: Strength
3 affected segregations + 0 unaffected segregations OR


2 affected segregations + 3 unaffected segregations
Gene: PAH (HGNC:8582)
Evidence Code: PP1 — Moderate
Modification Type: Strength
2 affected segregations + 0 unaffected segregations
Gene: PAH (HGNC:8582)
Evidence Code: PP1 — Supporting
Modification Type: Strength
1 affected family member + 3 unaffected segregations
Gene: PAH (HGNC:8582)
Evidence Code: PP3 — Strong
Modification Type: Strength
Applicable as described in Pejaver et al (PMID: 36413997): REVEL score ≥0.932 for missense variants


PP3 + PM1 should not exceed Strong
Gene: PAH (HGNC:8582)
Evidence Code: PP3 — Moderate
Modification Type: Strength
Applicable as described in Pejaver et al (PMID: 36413997): REVEL score 0.773 - 0.932 for missense variants
Gene: PAH (HGNC:8582)
Evidence Code: PP3 — Supporting
Modification Type: Strength
Applicable as described in Pejaver et al. (PMID: 36413997):




REVEL score of 0.644 - 0.733 for missense variants


In frame deletion or insertion predicted deleterious by 2 out of 3 tools (PROVEAN, MutationTaster, MutPred-InDel)


Predicted impact on splicing by SpliceAI (score >0.5)
Gene: PAH (HGNC:8582)
Evidence Code: PP4 — Moderate
Modification Type: Disease-specific,Strength
Plasma phenylalanine concentration persistently above 120 µmol/L (2mg/dL), and either normal urine pterins and normal DHPR activity, or sequencing of genes in the BH4 cofactor metabolism pathway to exclude a defect of BH4 cofactor metabolism.
Gene: PAH (HGNC:8582)
Evidence Code: PP4 — Supporting
Modification Type: Strength
A plasma phenylalanine concentration persistently above 120umol/L (2mg/dL) without analysis of urine pterins, DHPR activity, or sequencing to exclude defects of BH4 cofactor metabolism.
Gene: PAH (HGNC:8582)
Evidence Code: BA1 — Stand Alone
Modification Type: Disease-specific
An allele frequency ≥0.015 (1.5%), which is calculated with genetic heterogeneity of 90% to account for defects of BH4 metabolism, and penetrance of 80% to account for individuals who come to attention after becoming clinically symptomatic.
Gene: PAH (HGNC:8582)
Evidence Code: BS1 — Strong
Modification Type: Disease-specific
Allele frequency ≥0.002 (0.2%)
Gene: PAH (HGNC:8582)
Evidence Code: BS2 — Strong
Modification Type: None
Only to be used when variant is observed in the homozygous state in a healthy adult.
Gene: PAH (HGNC:8582)
Evidence Code: BS3 — Supporting
Modification Type: Disease-specific,Strength
In vitro enzyme activity >85% compared to wild type




Expression systems: placing the mutant (and wildtype) cDNA into plasmid vectors and introducing these into host cells. Transiently transfected human or other mammalian host cells are the closest available approximation to the in vivo situation (e.g., COS cells) (Trunzo, et al. Gene. 2016. 594:138-143).
Gene: PAH (HGNC:8582)
Evidence Code: BS4 — Strong
Modification Type: None
Applicable as described
Gene: PAH (HGNC:8582)
Evidence Code: BP4 — Strong
Modification Type: No change
Applicable as described in Pejaver et al.
Gene: PAH (HGNC:8582)
Evidence Code: BP4 — Moderate
Modification Type: No change
Applicable as described in Pejaver et al.
Gene: PAH (HGNC:8582)
Evidence Code: BP4 — Supporting
Modification Type: Gene-specific,None
Applicable as described in Pejaver et al.




REVEL score of 0.183 - 0.290 for missense variants


In frame deletion or insertion predicted benign by PROVEAN, MutationTaster, and MutPred-InDel


No predicted impact on splicing by SpliceAI (score <0.1)
Gene: PAH (HGNC:8582)
Evidence Code: BP5 — Supporting
Modification Type: No change
Applicable as described
Gene: PAH (HGNC:8582)
Evidence Code: BP7 — Strong
Modification Type: Strength
Applicable as described by Walker et al. (PMID: 36865205).
Gene: PAH (HGNC:8582)
Evidence Code: BP7 — Supporting
Modification Type: Gene-specific,None
Per SVI recommendations (PMID: 36865205), use BP7 only if BP4 is met; for variants with experimental evidence supporting that they do not alter splicing, use BP7_strong (RNA)




intronic variants must be outside +7/-21 nt


exonic variants must be outside first and last 3 bases of exon