U.S. flag

An official website of the United States government

NM_031307.4(PUS3):c.-47+3170T>C AND Hydrolethalus syndrome

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Feb 24, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000001202.7

Allele description [Variation Report for NM_031307.4(PUS3):c.-47+3170T>C]

NM_031307.4(PUS3):c.-47+3170T>C

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.-47+3170T>C
HGVS:
  • NC_000011.10:g.125900000A>G
  • NG_011842.1:g.21387A>G
  • NG_033067.1:g.8222T>C
  • NG_033067.2:g.8206T>C
  • NM_001134793.2:c.632A>GMANE SELECT
  • NM_001271985.2:c.-247+3170T>C
  • NM_001377269.1:c.632A>G
  • NM_001377270.1:c.632A>G
  • NM_001424364.1:c.632A>G
  • NM_031307.4:c.-47+3170T>CMANE SELECT
  • NM_145014.3:c.632A>G
  • NP_001128265.1:p.Asp211Gly
  • NP_001364198.1:p.Asp211Gly
  • NP_001364199.1:p.Asp211Gly
  • NP_001411293.1:p.Asp211Gly
  • NP_659451.1:p.Asp211Gly
  • NP_659451.1:p.Asp211Gly
  • NC_000011.9:g.125769895A>G
  • NM_145014.2:c.632A>G
  • Q96M11:p.Asp211Gly
Protein change:
D211G; ASP211GLY
Links:
UniProtKB: Q96M11#VAR_031867; OMIM: 610693.0001; dbSNP: rs104894232
NCBI 1000 Genomes Browser:
rs104894232
Molecular consequence:
  • NM_001271985.2:c.-247+3170T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_031307.4:c.-47+3170T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001134793.2:c.632A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377269.1:c.632A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377270.1:c.632A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001424364.1:c.632A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145014.3:c.632A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hydrolethalus syndrome (HLS)
Identifiers:
MONDO: MONDO:0006037; MedGen: C2931104; OMIM: PS236680

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001142427Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Pathogenic
(Jan 6, 2020) 		germlinecuration

SCV002082207Natera, Inc.
no assertion criteria provided
Pathogenic
(Feb 24, 2021) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Reproductive Health Research and Development, BGI Genomics, SCV001142427.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_145014.2:c.632A>G in the HYLS1 gene has an allele frequency of 0.01 in European (Finnish) subpopulation in the gnomAD database. The p.Asp211Gly (NM_145014.2:c.632A>G) variant has been observed in individuals with hydrolethalus syndrome and it has been reported to be a founder mutation in the Finnish population (PMID: 15843405; 18648327). Experimental studies have shown that this missense change causes mislocalization of the HYLS1 protein to the nucleus (PMID: 15843405). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS4; PS3.

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

From Natera, Inc., SCV002082207.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024