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

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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:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002073732	Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara	no assertion criteria provided	Pathogenic (Feb 8, 2022)	maternal	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002073732

Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara

no assertion criteria provided

Pathogenic
(Feb 8, 2022)

maternal

clinical testing

Summary from all submissions

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Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
European	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	European	1	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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