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NM_014489.4(PGAP2):c.391G>T (p.Glu131Ter) AND Hyperphosphatasia with intellectual disability syndrome 3

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 23, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001027671.3

Allele description [Variation Report for NM_014489.4(PGAP2):c.391G>T (p.Glu131Ter)]

NM_014489.4(PGAP2):c.391G>T (p.Glu131Ter)

Gene:
PGAP2:post-GPI attachment to proteins 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_014489.4(PGAP2):c.391G>T (p.Glu131Ter)
HGVS:
  • NC_000011.10:g.3823925G>T
  • NG_051812.1:g.31202G>T
  • NM_001145438.2:c.379G>T
  • NM_001256235.1:c.262G>T
  • NM_001256236.1:c.562G>T
  • NM_001256237.1:c.379G>T
  • NM_001256238.1:c.208G>T
  • NM_001256239.2:c.208G>T
  • NM_001256240.2:c.208G>T
  • NM_001283038.1:c.379G>T
  • NM_001283039.1:c.332G>T
  • NM_001283040.1:c.162-345G>T
  • NM_001346397.2:c.361G>T
  • NM_001346398.2:c.208G>T
  • NM_001346399.2:c.218G>T
  • NM_001346400.2:c.208G>T
  • NM_001346401.2:c.218G>T
  • NM_001346402.2:c.328G>T
  • NM_001346403.1:c.391G>T
  • NM_001346404.1:c.208G>T
  • NM_001346405.1:c.208G>T
  • NM_014489.4:c.391G>TMANE SELECT
  • NP_001138910.1:p.Glu127Ter
  • NP_001243164.1:p.Glu88Ter
  • NP_001243165.1:p.Glu188Ter
  • NP_001243166.1:p.Glu127Ter
  • NP_001243167.1:p.Glu70Ter
  • NP_001243168.1:p.Glu70Ter
  • NP_001243169.1:p.Glu70Ter
  • NP_001269967.1:p.Glu127Ter
  • NP_001269968.1:p.Gly111Val
  • NP_001333326.1:p.Glu121Ter
  • NP_001333327.1:p.Glu70Ter
  • NP_001333328.1:p.Gly73Val
  • NP_001333329.1:p.Glu70Ter
  • NP_001333330.1:p.Gly73Val
  • NP_001333331.1:p.Glu110Ter
  • NP_001333332.1:p.Glu131Ter
  • NP_001333333.1:p.Glu70Ter
  • NP_001333334.1:p.Glu70Ter
  • NP_055304.1:p.Glu131Ter
  • NC_000011.9:g.3845155G>T
  • NM_014489.2:c.391G>T
  • NR_027016.3:n.135G>T
  • NR_027017.4:n.528G>T
  • NR_027018.2:n.356G>T
  • NR_045923.2:n.150G>T
  • NR_045927.2:n.150G>T
  • NR_045929.2:n.263G>T
  • NR_104270.2:n.150G>T
  • NR_104271.2:n.410G>T
  • NR_104272.2:n.135G>T
  • NR_144427.2:n.150G>T
  • NR_144428.2:n.395G>T
  • NR_144429.2:n.135G>T
Protein change:
E110*
Links:
dbSNP: rs1590414630
NCBI 1000 Genomes Browser:
rs1590414630
Molecular consequence:
  • NM_001283040.1:c.162-345G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001283039.1:c.332G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346399.2:c.218G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346401.2:c.218G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027016.3:n.135G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_027017.4:n.528G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_027018.2:n.356G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045923.2:n.150G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045927.2:n.150G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045929.2:n.263G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104270.2:n.150G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104271.2:n.410G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104272.2:n.135G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144427.2:n.150G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144428.2:n.395G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144429.2:n.135G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001145438.2:c.379G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256235.1:c.262G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256236.1:c.562G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256237.1:c.379G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256238.1:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256239.2:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001256240.2:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001283038.1:c.379G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346397.2:c.361G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346398.2:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346400.2:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346402.2:c.328G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346403.1:c.391G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346404.1:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001346405.1:c.208G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_014489.4:c.391G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Hyperphosphatasia with intellectual disability syndrome 3 (HPMRS3)
Synonyms:
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 21; GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 8; HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 3
Identifiers:
MONDO: MONDO:0013628; MedGen: C3280153; Orphanet: 247262; OMIM: 614207

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001190233Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 23, 2019) 		paternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedpaternalyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Facile, rapid, and large-area periodic patterning of semiconductor substrates with submicron inorganic structures.

Kempa TJ, Bediako DK, Jones EC, Lieber CM, Nocera DG.

J Am Chem Soc. 2015 Mar 25;137(11):3739-42. doi: 10.1021/ja5118717. Epub 2015 Mar 12.

PubMed [citation]
PMID:
25741869

Details of each submission

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV001190233.1

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

Last Updated: Jun 23, 2024