NM_001012339.3(DNAJC21):c.15T>G (p.Tyr5Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 3, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003682166.2

Allele description [Variation Report for NM_001012339.3(DNAJC21):c.15T>G (p.Tyr5Ter)]

NM_001012339.3(DNAJC21):c.15T>G (p.Tyr5Ter)

Genes:

LOC129993792:ATAC-STARR-seq lymphoblastoid silent region 15969 [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.15T>G (p.Tyr5Ter)

HGVS:

NC_000005.10:g.34929834T>G
NG_052822.1:g.5295T>G
NG_173237.1:g.220T>G
NG_173238.1:g.120T>G
NM_001012339.3:c.15T>GMANE SELECT
NM_001348420.2:c.15T>G
NM_194283.4:c.15T>G
NP_001012339.2:p.Tyr5Ter
NP_001335349.1:p.Tyr5Ter
NP_919259.3:p.Tyr5Ter
LRG_1214t1:c.15T>G
LRG_1214:g.5295T>G
LRG_1214p1:p.Tyr5Ter
NC_000005.9:g.34929939T>G

Protein change:

Y5*

Molecular consequence:

NM_001012339.3:c.15T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001348420.2:c.15T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_194283.4:c.15T>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004404931	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 3, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 27346687, 28062395, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004404931

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 3, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

DNAJC21 Mutations Link a Cancer-Prone Bone Marrow Failure Syndrome to Corruption in 60S Ribosome Subunit Maturation.

Tummala H, Walne AJ, Williams M, Bockett N, Collopy L, Cardoso S, Ellison A, Wynn R, Leblanc T, Fitzgibbon J, Kelsell DP, van Heel DA, Payne E, Plagnol V, Dokal I, Vulliamy T.

Am J Hum Genet. 2016 Jul 7;99(1):115-24. doi: 10.1016/j.ajhg.2016.05.002. Epub 2016 Jun 23.

PubMed [citation]

PMID:: 27346687
PMCID:: PMC5005432

Biallelic mutations in DNAJC21 cause Shwachman-Diamond syndrome.

Dhanraj S, Matveev A, Li H, Lauhasurayotin S, Jardine L, Cada M, Zlateska B, Tailor CS, Zhou J, Mendoza-Londono R, Vincent A, Durie PR, Scherer SW, Rommens JM, Heon E, Dror Y.

Blood. 2017 Mar 16;129(11):1557-1562. doi: 10.1182/blood-2016-08-735431. Epub 2017 Jan 6. No abstract available.

PubMed [citation]

PMID:: 28062395

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004404931.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DNAJC21-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Tyr5*) in the DNAJC21 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNAJC21 are known to be pathogenic (PMID: 27346687, 28062395).

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

Last Updated: Sep 29, 2024

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