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NM_001015880.2(PAPSS2):c.712C>T (p.Arg238Ter) AND Spondyloepimetaphyseal dysplasia, PAPSS2 type

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 4, 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:
RCV003388605.1

Allele description [Variation Report for NM_001015880.2(PAPSS2):c.712C>T (p.Arg238Ter)]

NM_001015880.2(PAPSS2):c.712C>T (p.Arg238Ter)

Gene:
PAPSS2:3'-phosphoadenosine 5'-phosphosulfate synthase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_001015880.2(PAPSS2):c.712C>T (p.Arg238Ter)
Other names:
p.(Arg238*)
HGVS:
  • NC_000010.11:g.87715057C>T
  • NG_012150.1:g.60339C>T
  • NM_001015880.2:c.712C>TMANE SELECT
  • NM_004670.4:c.712C>T
  • NP_001015880.1:p.Arg238Ter
  • NP_004661.2:p.Arg238Ter
  • NC_000010.10:g.89474814C>T
Protein change:
R238*
Links:
dbSNP: rs541008862
NCBI 1000 Genomes Browser:
rs541008862
Molecular consequence:
  • NM_001015880.2:c.712C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004670.4:c.712C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
3

Condition(s)

Name:
Spondyloepimetaphyseal dysplasia, PAPSS2 type
Synonyms:
SEMD, PAKISTANI TYPE; Spondyloepimetaphyseal dysplasia, pakistani type; BRACHYOLMIA TYPE 4 WITH MILD EPIPHYSEAL AND METAPHYSEAL CHANGES
Identifiers:
MONDO: MONDO:0019666; MedGen: C2748515; Orphanet: 93282; OMIM: 612847

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004100667Center of Genomic medicine, Geneva, University Hospital of Geneva
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 4, 2023)
inheritedclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyes3not providednot providednot providednot providedclinical 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 Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV004100667.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testing PubMed (1)

Description

This variant was identified in a homozygous state (inherited from both parents) in an affected patient.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided3not providednot providednot provided

Last Updated: Oct 20, 2024