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NM_031307.4(PUS3):c.578G>A (p.Arg193Gln) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 10, 2022
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:
RCV002462130.1

Allele description [Variation Report for NM_031307.4(PUS3):c.578G>A (p.Arg193Gln)]

NM_031307.4(PUS3):c.578G>A (p.Arg193Gln)

Genes:
HYLS1:HYLS1 centriolar and ciliogenesis associated [Gene - OMIM - HGNC]
PUS3:pseudouridine synthase 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q24.2
Genomic location:
Preferred name:
NM_031307.4(PUS3):c.578G>A (p.Arg193Gln)
HGVS:
  • NC_000011.10:g.125895590C>T
  • NG_011842.1:g.16977C>T
  • NG_033067.1:g.12632G>A
  • NG_033067.2:g.12616G>A
  • NM_001134793.2:c.-25-3754C>TMANE SELECT
  • NM_001271985.2:c.-47G>A
  • NM_001377269.1:c.-25-3754C>T
  • NM_001377270.1:c.-22-3757C>T
  • NM_001424364.1:c.-22-3757C>T
  • NM_031307.4:c.578G>AMANE SELECT
  • NM_145014.3:c.-80-3514C>T
  • NP_112597.4:p.Arg193Gln
  • NC_000011.9:g.125765485C>T
  • NM_031307.3:c.578G>A
Protein change:
R193Q
Links:
dbSNP: rs576405108
NCBI 1000 Genomes Browser:
rs576405108
Molecular consequence:
  • NM_001271985.2:c.-47G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001134793.2:c.-25-3754C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377269.1:c.-25-3754C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377270.1:c.-22-3757C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001424364.1:c.-22-3757C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_145014.3:c.-80-3514C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_031307.4:c.578G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002756866GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(May 10, 2022)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV002756866.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Observed with a second PUS3 variant in unrelated patients with clinical features including intellectual disability, brain abnormalities, hypotonia, and/or epilepsy in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes in some cases (Aldinger et al., 2019; Nostvik et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 31474318, 34415064)

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

Last Updated: Aug 30, 2025