NM_017837.4(PIGV):c.146C>A (p.Ser49Ter) AND Hyperphosphatasia with intellectual disability syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 15, 2023
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:: RCV003387542.1

Allele description [Variation Report for NM_017837.4(PIGV):c.146C>A (p.Ser49Ter)]

NM_017837.4(PIGV):c.146C>A (p.Ser49Ter)

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.146C>A (p.Ser49Ter)

HGVS:

NC_000001.11:g.26794180C>A
NG_028133.1:g.11218C>A
NM_001202554.2:c.146C>A
NM_001374478.1:c.146C>A
NM_001374480.1:c.146C>A
NM_001374481.1:c.146C>A
NM_001374482.1:c.146C>A
NM_001374483.1:c.-236C>A
NM_001374484.1:c.146C>A
NM_001374485.1:c.146C>A
NM_001374486.1:c.78+3287C>A
NM_017837.4:c.146C>AMANE SELECT
NP_001189483.1:p.Ser49Ter
NP_001361407.1:p.Ser49Ter
NP_001361409.1:p.Ser49Ter
NP_001361410.1:p.Ser49Ter
NP_001361411.1:p.Ser49Ter
NP_001361413.1:p.Ser49Ter
NP_001361414.1:p.Ser49Ter
NP_060307.2:p.Ser49Ter
NC_000001.10:g.27120671C>A
NM_017837.3:c.146C>A
NR_164651.1:n.644C>A
NR_164652.1:n.522C>A

Protein change:

S49*

Links:

dbSNP: rs145160045

NCBI 1000 Genomes Browser:

rs145160045

Molecular consequence:

NM_001374483.1:c.-236C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374486.1:c.78+3287C>A - intron variant - [Sequence Ontology: SO:0001627]
NR_164651.1:n.644C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164652.1:n.522C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001202554.2:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374478.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374480.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374481.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374482.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374484.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001374485.1:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_017837.4:c.146C>A - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004099144	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 15, 2023)	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

SCV004099144

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 15, 2023)

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	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

Details of each submission

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV004099144.1

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

Description

PVS1, PM2, PM3

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

Last Updated: Mar 10, 2024

ClinVar

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