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NM_014489.4(PGAP2):c.395T>G (p.Val132Gly) AND Hyperphosphatasia with intellectual disability syndrome 3

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 28, 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:
RCV000988478.1

Allele description [Variation Report for NM_014489.4(PGAP2):c.395T>G (p.Val132Gly)]

NM_014489.4(PGAP2):c.395T>G (p.Val132Gly)

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.395T>G (p.Val132Gly)
HGVS:
  • NC_000011.10:g.3823929T>G
  • NG_051812.1:g.31206T>G
  • NM_001145438.2:c.383T>G
  • NM_001256235.1:c.266T>G
  • NM_001256236.1:c.566T>G
  • NM_001256237.1:c.383T>G
  • NM_001256238.1:c.212T>G
  • NM_001256239.2:c.212T>G
  • NM_001256240.2:c.212T>G
  • NM_001283038.1:c.383T>G
  • NM_001283039.1:c.336T>G
  • NM_001283040.1:c.162-341T>G
  • NM_001346397.2:c.365T>G
  • NM_001346398.2:c.212T>G
  • NM_001346399.2:c.222T>G
  • NM_001346400.2:c.212T>G
  • NM_001346401.2:c.222T>G
  • NM_001346402.2:c.332T>G
  • NM_001346403.1:c.395T>G
  • NM_001346404.1:c.212T>G
  • NM_001346405.1:c.212T>G
  • NM_014489.4:c.395T>GMANE SELECT
  • NP_001138910.1:p.Val128Gly
  • NP_001243164.1:p.Val89Gly
  • NP_001243165.1:p.Val189Gly
  • NP_001243166.1:p.Val128Gly
  • NP_001243167.1:p.Val71Gly
  • NP_001243168.1:p.Val71Gly
  • NP_001243169.1:p.Val71Gly
  • NP_001269967.1:p.Val128Gly
  • NP_001269968.1:p.Gly112=
  • NP_001333326.1:p.Val122Gly
  • NP_001333327.1:p.Val71Gly
  • NP_001333328.1:p.Gly74=
  • NP_001333329.1:p.Val71Gly
  • NP_001333330.1:p.Gly74=
  • NP_001333331.1:p.Val111Gly
  • NP_001333332.1:p.Val132Gly
  • NP_001333333.1:p.Val71Gly
  • NP_001333334.1:p.Val71Gly
  • NP_055304.1:p.Val132Gly
  • NC_000011.9:g.3845159T>G
  • NR_027016.3:n.139T>G
  • NR_027017.4:n.532T>G
  • NR_027018.2:n.360T>G
  • NR_045923.2:n.154T>G
  • NR_045927.2:n.154T>G
  • NR_045929.2:n.267T>G
  • NR_104270.2:n.154T>G
  • NR_104271.2:n.414T>G
  • NR_104272.2:n.139T>G
  • NR_144427.2:n.154T>G
  • NR_144428.2:n.399T>G
  • NR_144429.2:n.139T>G
Protein change:
V111G
Links:
dbSNP: rs551147697
NCBI 1000 Genomes Browser:
rs551147697
Molecular consequence:
  • NM_001283040.1:c.162-341T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145438.2:c.383T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256235.1:c.266T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256236.1:c.566T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256237.1:c.383T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256238.1:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256239.2:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256240.2:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001283038.1:c.383T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346397.2:c.365T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346398.2:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346400.2:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346402.2:c.332T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346403.1:c.395T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346404.1:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346405.1:c.212T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014489.4:c.395T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_027016.3:n.139T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_027017.4:n.532T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_027018.2:n.360T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045923.2:n.154T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045927.2:n.154T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045929.2:n.267T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104270.2:n.154T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104271.2:n.414T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104272.2:n.139T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144427.2:n.154T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144428.2:n.399T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144429.2:n.139T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001283039.1:c.336T>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001346399.2:c.222T>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001346401.2:c.222T>G - synonymous variant - [Sequence Ontology: SO:0001819]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001138211Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)		Uncertain significance
(May 28, 2019) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Mendelics, SCV001138211.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 5, 2023