NM_017837.4(PIGV):c.115G>A (p.Glu39Lys) AND Hyperphosphatasia with intellectual disability syndrome 1

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 4, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000765106.13

Allele description [Variation Report for NM_017837.4(PIGV):c.115G>A (p.Glu39Lys)]

NM_017837.4(PIGV):c.115G>A (p.Glu39Lys)

Gene:

PIGV:phosphatidylinositol glycan anchor biosynthesis class V [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.11

Genomic location:

Preferred name:

NM_017837.4(PIGV):c.115G>A (p.Glu39Lys)

HGVS:

NC_000001.11:g.26794149G>A
NG_028133.1:g.11187G>A
NM_001202554.2:c.115G>A
NM_001374478.1:c.115G>A
NM_001374480.1:c.115G>A
NM_001374481.1:c.115G>A
NM_001374482.1:c.115G>A
NM_001374483.1:c.-267G>A
NM_001374484.1:c.115G>A
NM_001374485.1:c.115G>A
NM_001374486.1:c.78+3256G>A
NM_017837.4:c.115G>AMANE SELECT
NP_001189483.1:p.Glu39Lys
NP_001189483.1:p.Glu39Lys
NP_001361407.1:p.Glu39Lys
NP_001361409.1:p.Glu39Lys
NP_001361410.1:p.Glu39Lys
NP_001361411.1:p.Glu39Lys
NP_001361413.1:p.Glu39Lys
NP_001361414.1:p.Glu39Lys
NP_060307.2:p.Glu39Lys
NP_060307.2:p.Glu39Lys
NC_000001.10:g.27120640G>A
NM_001202554.1:c.115G>A
NM_001202554.1:c.115G>A
NM_017837.3:c.115G>A
NR_164651.1:n.613G>A
NR_164652.1:n.491G>A

Protein change:

E39K

Links:

dbSNP: rs369275802

NCBI 1000 Genomes Browser:

rs369275802

Molecular consequence:

NM_001374483.1:c.-267G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374486.1:c.78+3256G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001202554.2:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374478.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374480.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374481.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374482.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374484.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374485.1:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017837.4:c.115G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164651.1:n.613G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164652.1:n.491G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hyperphosphatasia with intellectual disability syndrome 1 (HPMRS1)
Synonyms:: MABRY SYNDROME; GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 2; HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 1
Identifiers:: MONDO: MONDO:0009398; MedGen: C4551502; Orphanet: 247262; OMIM: 239300

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Homo sapiens novel C2H2 type zinc finger protein (MGC10715), mRNA
Homo sapiens novel C2H2 type zinc finger protein (MGC10715), mRNA
gi|23503322|ref|NM_024325.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000896328	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 31, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001522589	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 27, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004810004	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 4, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000896328

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 31, 2018)

unknown

clinical testing

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

SCV001522589

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 27, 2020)

unknown

clinical testing

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

SCV004810004

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 4, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV000896328.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001522589.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810004.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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