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NM_001127178.3(PIGG):c.1633T>C (p.Ser545Pro) AND Intellectual disability, autosomal recessive 53

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 9, 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:
RCV000821363.6

Allele description [Variation Report for NM_001127178.3(PIGG):c.1633T>C (p.Ser545Pro)]

NM_001127178.3(PIGG):c.1633T>C (p.Ser545Pro)

Gene:
PIGG:phosphatidylinositol glycan anchor biosynthesis class G (EMM blood group) [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.3
Genomic location:
Preferred name:
NM_001127178.3(PIGG):c.1633T>C (p.Ser545Pro)
HGVS:
  • NC_000004.12:g.523477T>C
  • NG_051621.1:g.29278T>C
  • NM_001127178.3:c.1633T>CMANE SELECT
  • NM_001289051.2:c.1366T>C
  • NM_001289052.2:c.1234T>C
  • NM_001345986.2:c.1366T>C
  • NM_001345987.2:c.1342T>C
  • NM_001345988.2:c.604T>C
  • NM_001345990.2:c.100T>C
  • NM_001345991.2:c.100T>C
  • NM_001345994.2:c.535T>C
  • NM_017733.5:c.1609T>C
  • NP_001120650.1:p.Ser545Pro
  • NP_001275980.1:p.Ser456Pro
  • NP_001275981.1:p.Ser412Pro
  • NP_001332915.1:p.Ser456Pro
  • NP_001332916.1:p.Ser448Pro
  • NP_001332917.1:p.Ser202Pro
  • NP_001332919.1:p.Ser34Pro
  • NP_001332920.1:p.Ser34Pro
  • NP_001332923.1:p.Ser179Pro
  • NP_060203.3:p.Ser537Pro
  • NC_000004.11:g.517266T>C
  • NM_001127178.2:c.1633T>C
  • NR_110293.2:n.1713T>C
  • NR_144326.2:n.1995T>C
  • NR_144327.2:n.1759T>C
  • NR_144328.2:n.2182T>C
  • NR_144329.2:n.1949T>C
  • NR_144330.2:n.1759T>C
  • NR_144331.2:n.1995T>C
Protein change:
S179P
Links:
dbSNP: rs1577104001
NCBI 1000 Genomes Browser:
rs1577104001
Molecular consequence:
  • NM_001127178.3:c.1633T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289051.2:c.1366T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289052.2:c.1234T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345986.2:c.1366T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345987.2:c.1342T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345988.2:c.604T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345990.2:c.100T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345991.2:c.100T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001345994.2:c.535T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017733.5:c.1609T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110293.2:n.1713T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144326.2:n.1995T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144327.2:n.1759T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144328.2:n.2182T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144329.2:n.1949T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144330.2:n.1759T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144331.2:n.1995T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Intellectual disability, autosomal recessive 53 (NEDHSCA)
Synonyms:
GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 13; Mental retardation, autosomal recessive 53; NEURODEVELOPMENTAL DISORDER WITH OR WITHOUT HYPOTONIA, SEIZURES, AND CEREBELLAR ATROPHY
Identifiers:
MONDO: MONDO:0014832; MedGen: C4310794; OMIM: 616917

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000962118Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 9, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000962118.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PIGG protein function. ClinVar contains an entry for this variant (Variation ID: 663484). This variant has not been reported in the literature in individuals affected with PIGG-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 545 of the PIGG protein (p.Ser545Pro).

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

Last Updated: Feb 20, 2024