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NM_001012339.3(DNAJC21):c.148C>T (p.Gln50Ter) AND Bone marrow failure syndrome 3

Clinical significance:Pathogenic (Last evaluated: Feb 8, 2022)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001824280.1

Allele description [Variation Report for NM_001012339.3(DNAJC21):c.148C>T (p.Gln50Ter)]

NM_001012339.3(DNAJC21):c.148C>T (p.Gln50Ter)

Gene:
DNAJC21:DnaJ heat shock protein family (Hsp40) member C21 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_001012339.3(DNAJC21):c.148C>T (p.Gln50Ter)
HGVS:
  • NC_000005.10:g.34933865C>T
  • NG_052822.1:g.9326C>T
  • NM_001012339.3:c.148C>TMANE SELECT
  • NM_001348420.2:c.148C>T
  • NM_194283.4:c.148C>T
  • NP_001012339.2:p.Gln50Ter
  • NP_001335349.1:p.Gln50Ter
  • NP_919259.3:p.Gln50Ter
  • LRG_1214t1:c.148C>T
  • LRG_1214:g.9326C>T
  • LRG_1214p1:p.Gln50Ter
  • NC_000005.9:g.34933970C>T
Protein change:
Q50*
Molecular consequence:
  • NM_001012339.3:c.148C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001348420.2:c.148C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_194283.4:c.148C>T - nonsense - [Sequence Ontology: SO:0001587]
Functional consequence:
functionally_abnormal [Sequence Ontology: SO:0002218]
Observations:
1

Condition(s)

Name:
Bone marrow failure syndrome 3 (BMFS3)
Identifiers:
MONDO: MONDO:0014887; MedGen: C4310744; OMIM: 617052

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002073732Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoarano assertion criteria providedPathogenic
(Feb 8, 2022)
maternalclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Europeanmaternalyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara, SCV002073732.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European1not providednot providedclinical testingnot provided

Description

This null variant has been observed in compound heterozigosity with another pathogenic variant in a patient with Bone marrow failure syndrome 3. PVS2 Very Strong: Null variant (nonsense), in gene DNAJC21 for which loss-of-function is a known mechanism of disease, associated with Bone marrow failure syndrome 3. PM2 Strong: Using strength Strong because the position is highly conserved (phyloP100way = 7.35 is greater than 7.2). Variant not found in gnomAD exomes. Variant not found in gnomAD genomes (good gnomAD genomes coverage = 31.1). PP3 Supporting: Pathogenic computational verdict based on 5 pathogenic predictions from BayesDel_addAF, DANN, EIGEN, FATHMM-MKL and MutationTaster vs no benign predictions.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 23, 2022