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

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2
First in ClinVar:
Feb 11, 2022
Most recent Submission:
Mar 28, 2022
Last evaluated:
Dec 8, 2021
Accession:
VCV001339571.2
Variation ID:
1339571
Description:
single nucleotide variant
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NM_001012339.3(DNAJC21):c.148C>T (p.Gln50Ter)

Allele ID
1330717
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p13.2
Genomic location
5: 34933865 (GRCh38) GRCh38 UCSC
5: 34933970 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001012339.3:c.148C>T MANE Select NP_001012339.2:p.Gln50Ter nonsense
NM_001348420.2:c.148C>T NP_001335349.1:p.Gln50Ter nonsense
NM_194283.4:c.148C>T NP_919259.3:p.Gln50Ter nonsense
... more HGVS
Protein change
Q50*
Other names
-
Canonical SPDI
NC_000005.10:34933864:C:T
Functional consequence
functionally_abnormal [Sequence Ontology SO:0002218]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Dec 8, 2021 RCV001869834.1
Pathogenic 1 no assertion criteria provided Feb 8, 2022 RCV001824280.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DNAJC21 Little evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
209 236

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(Dec 08, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV002195890.1
First in ClinVar: Mar 28, 2022
Last updated: Mar 28, 2022
Publications:
PubMed (2)
PubMed: 2734668728062395
Comment:
This sequence change creates a premature translational stop signal (p.Gln50*) in the DNAJC21 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Feb 08, 2022)
no assertion criteria provided
Method: clinical testing
Bone marrow failure syndrome 3
(Autosomal recessive inheritance)
Affected status: yes
Allele origin: maternal
Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara
Accession: SCV002073732.1
First in ClinVar: Feb 11, 2022
Last updated: Feb 11, 2022
Comment:
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: … (more)
Clinical Features:
Retinal dystrophy (present) , Failure to thrive (present) , Fetal growth restriction (present) , Myopia (present) , Cryptorchidism (present) , Pancytopenia (present) , Joint hypermobility … (more)
Zygosity: 1 Compound Heterozygote
Age: 0-9 years
Sex: male
Ethnicity/Population group: European
Method: WGS
Testing laboratory: Invitae
Date variant was reported to submitter: 2021-11-04
Testing laboratory interpretation: Pathogenic

Functional evidence

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Functional consequence Method Result Submitter Supporting information
functionally_abnormal
Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara
Accession: SCV002073732.1
Submitted: (Feb 08, 2022)
Evidence details

Citations for this variant

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Title Author Journal Year Link
Biallelic mutations in DNAJC21 cause Shwachman-Diamond syndrome. Dhanraj S Blood 2017 PMID: 28062395
DNAJC21 Mutations Link a Cancer-Prone Bone Marrow Failure Syndrome to Corruption in 60S Ribosome Subunit Maturation. Tummala H American journal of human genetics 2016 PMID: 27346687

Record last updated Apr 25, 2022