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NM_000277.2(PAH):c.284_286delTCA (p.Ile95del) AND Phenylketonuria

Germline classification:
Conflicting classifications of pathogenicity (3 submissions)
Last evaluated:
May 19, 2016
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000000635.4

Allele description

NM_000277.2(PAH):c.284_286delTCA (p.Ile95del)

Gene:
PAH:phenylalanine hydroxylase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q23.2
Genomic location:
Preferred name:
NM_000277.2(PAH):c.284_286delTCA (p.Ile95del)
HGVS:
  • NC_000012.12:g.102894801_102894803delTGA
  • NG_008690.2:g.68608_68610delTCA
  • NM_000277.2:c.284_286delTCA
  • NP_000268.1:p.Ile95del
  • NC_000012.11:g.103288579_103288581delTGA
  • NM_000277.1:c.283_285delATC
  • NM_000277.1:c.284_286del
  • NM_000277.1:c.284_286delTCA
  • p.I95del
Protein change:
I95del
Links:
OMIM: 612349.0030; dbSNP: rs62508727
NCBI 1000 Genomes Browser:
rs62508727
Allele Frequency:
0.00003(-)
Molecular consequence:
  • NM_000277.1:c.284_286delTCA - inframe_variant - [Sequence Ontology: SO:0001650]
Observations:
2

Condition(s)

Name:
Phenylketonuria (PKU)
Synonyms:
Phenylketonurias; Classic phenylketonuria
Identifiers:
MedGen: C0031485; Orphanet: 716; OMIM: 261600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020785OMIM
no assertion criteria provided
Pathogenic
(Aug 15, 2007)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000110374EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
criteria provided, single submitter

(EGL Classification Definitions)
Pathogenic
(Feb 6, 2013)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000485292Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(May 19, 2016)
unknownclinical testing

PubMed (12)
[See all records that cite these PMIDs]

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknown2not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Phenylalanine hydroxylase deficiency exhibits mutation heterogeneity in two large old order Amish settlements.

Wang H, Nye L, Puffenberger E, Morton H.

Am J Med Genet A. 2007 Aug 15;143A(16):1938-40. No abstract available.

PubMed [citation]
PMID:
17630668

Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.

Bean LJ, Tinker SW, da Silva C, Hegde MR.

Hum Mutat. 2013 Sep;34(9):1183-8. doi: 10.1002/humu.22364. Epub 2013 Aug 5.

PubMed [citation]
PMID:
23757202
See all PubMed Citations (14)

Details of each submission

From OMIM, SCV000020785.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In a patient with mild phenylketonuria (PKU; 261600), Caillaud et al. (1991) reported a 3-bp in-frame deletion resulting in loss of isoleucine-94. The mutant enzyme showed markedly reduced affinity for phenylalanine. Since the deletion was located in the third exon of the gene, which shows no homology with other hydroxylases, Caillaud et al. (1991) suggested that exon 3 is involved in the specificity of PAH for phenylalanine. It appeared that this mutation may have occurred recently on the background of a haplotype II gene in Portugal.

In patients with PKU from the Old Order Amish in Lancaster County, Pennsylvania, Wang et al. (2007) identified compound heterozygosity for 2 PAH mutations: R261Q (612349.0006) and the 3-bp deletion at codon 94. The incidence of PKU in the Lancaster County Amish was 1 in 10,000, similar to that in other populations.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000110374.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From Counsyl, SCV000485292.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (12)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 19, 2017