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NM_001012339.3(DNAJC21):c.643_644delinsTTT (p.Lys215fs) 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:
RCV001824282.1

Allele description [Variation Report for NM_001012339.3(DNAJC21):c.643_644delinsTTT (p.Lys215fs)]

NM_001012339.3(DNAJC21):c.643_644delinsTTT (p.Lys215fs)

Gene:
DNAJC21:DnaJ heat shock protein family (Hsp40) member C21 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_001012339.3(DNAJC21):c.643_644delinsTTT (p.Lys215fs)
HGVS:
  • NC_000005.10:g.34937530_34937531delinsTTT
  • NG_052822.1:g.12991_12992delinsTTT
  • NM_001012339.3:c.643_644delinsTTTMANE SELECT
  • NM_001348420.2:c.643_644delinsTTT
  • NM_194283.4:c.643_644delinsTTT
  • NP_001012339.2:p.Lys215fs
  • NP_001335349.1:p.Lys215fs
  • NP_919259.3:p.Lys215fs
  • LRG_1214t1:c.643_644delinsTTT
  • LRG_1214:g.12991_12992delinsTTT
  • LRG_1214p1:p.Lys215fs
  • NC_000005.9:g.34937635_34937636delinsTTT
Protein change:
K215fs
Molecular consequence:
  • NM_001012339.3:c.643_644delinsTTT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001348420.2:c.643_644delinsTTT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_194283.4:c.643_644delinsTTT - frameshift variant - [Sequence Ontology: SO:0001589]
Functional consequence:
No function
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
SCV002073733Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoarano assertion criteria providedPathogenic
(Feb 8, 2022)
paternalclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Europeanpaternalyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara, SCV002073733.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European1not providednot providedclinical testingnot provided

Description

Null variant observed in compound heterozygosity with another pathogenic variant in a male affected by Bone marrow failure syndrome 3. PVS1 Very Strong: Null variant (frame-shift), in gene DNAJC21 for which loss-of-function is a known mechanism of disease (gene has 9 pathogenic LOF variants and gnomAD Loss-of-Function Observed/Expected = 0.48 is less than 0.755), associated with Bone marrow failure syndrome 3. PM2 Moderate: Variant not found in gnomAD exomes. Variant not found in gnomAD genomes (good gnomAD genomes coverage = 31.6).

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

Last Updated: Apr 23, 2022