NM_000277.3:c.975C>G

Variant names:

• chr12-102844426-G-C
• rs62508573
• NM_000277.3:c.975C>G

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM3 PM2 PP4_Moderate PVS1

This summary comes from the ClinGen Evidence Repository: The c.975C>G (p.Tyr325Ter) is a variant in PAH is a null variant (nonsense variant) in a gene where LOF is a known mechanism of disease, leading to premature truncation and NMD (PVS1). It is present at extremely low frequencies in ethnically diverse control databases (gnomAD AF 0.00000399; PAH PM2 cutoff: <0.0002) (PM2). It has been identified in at least 13 PKU probands, at least 5 of whom BH4 deficiency was formally excluded (PP4_Moderate), including in trans with pathogenic or likely pathogenic variants in 9 cases, in trans with VUS in two cases, and homozygous in two cases (PM3_VeryStrong). It was first identified in a Korean patient with classic PKU (as confirmed by blood Phe levels) in trans with the N207D variant (pathogenic per PAH VCEP) (PMID:9452061; PMID:15503242); BH4 deficiency was excluded by urinary pterin analysis and DPHR assay. It was also found in another four patients with PKU, BH4 deficiency was excluded by urinary pterin analysis and DPHR assay (PMID:15503242): one in trans with the known pathogenic (per PAH VCEP and in Clinvar) p.R413P variant (patient’s PKU phenotype not specified); one with classic PKU in trans with the known pathogenic (per PAH VCEP) p.V388M variant; one with mild hyperphenylalanemia in trans with the ClinVar pathogenic p.Y204C variant; and one in trans with the known pathogenic (per PAH VCEP) p. R243Q variant (PKU phenotype not specified). It has also been found in a Hispanic patient with classic PKU and BH4 deficiency excluded in trans with the pathogenic (per PAH VCEP) p.R261X variant (PMID:23430918). It has also been found in 9 Chinese PKU cases (PMID:26503515; PMID:30050108), BH4 deficiency does not appear to have been ruled out: 2 homozygotes (classic PKU); one classic PKU case in trans with p.EX6-96A>G variant (pathogenic per PAH VCEP); one classic PKU case in trans with c.843-14_-11delCTTT (no PAH VCEP classification); one mild PKU case in trans with p.A434D (pathogenic per PAH VCEP); one mild hyperphenylalanemia case in trans with p.R241C (ClinVar pathogenic, PAH VCEP pathogenic); one classic PKU case in trans with p.Y206C (Likely pathogenic per PAH VCEP); and one mild hyperphenylalanemia case in trans with p.T418P (VUS per PAH VCEP). It is also listed Pathogenic in ClinVar by two labs (variant ID 102921). Classification: PathogenicSupporting Criteria: PVS1, PM2; PM3_VeryStrong; PP4_Moderate LINK:https://erepo.genome.network/evrepo/ui/classification/CA229885/MONDO:0009861/006

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: PAH NM_000277.3 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:4 O:1
• Conservation: PhyloP100: 3.33
• Publications: 4 publications found

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), ClinGen, Myriad Women’s Health, G2P
• 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

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000277.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAH	NM_000277.3	MANE Select	c.975C>G	p.Tyr325*	stop_gained	Exon 10 of 13	NP_000268.1	P00439
	PAH	NM_001354304.2		c.975C>G	p.Tyr325*	stop_gained	Exon 11 of 14	NP_001341233.1	P00439

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAH	ENST00000553106.6	TSL:1 MANE Select	c.975C>G	p.Tyr325*	stop_gained	Exon 10 of 13	ENSP00000448059.1	P00439
	PAH	ENST00000906695.1		c.1074C>G	p.Tyr358*	stop_gained	Exon 11 of 14	ENSP00000576754.1
	PAH	ENST00000906692.1		c.1053C>G	p.Tyr351*	stop_gained	Exon 10 of 13	ENSP00000576751.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000399 AC: 1 AN: 250614 AF XY: 0.00000739

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457936 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 725522

African (AFR) AF: 0.00 AC: 0 AN: 33386

American (AMR) AF: 0.00 AC: 0 AN: 44652

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26088

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39686

South Asian (SAS) AF: 0.00 AC: 0 AN: 86118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53372

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5760

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1108634

Other (OTH) AF: 0.00 AC: 0 AN: 60240

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
4	-	-	Phenylketonuria (4)
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	40
DANN	Uncertain	1.0
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.36
FATHMM_MKL	Uncertain	0.96	D
PhyloP100		3.3
Vest4		0.94
GERP RS		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.33		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.33		Position offset: 5

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

Other links and lift over

dbSNP: rs62508573; hg19: chr12-103238204;