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

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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:

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
SCV002073733	Center of Genomic Medicine,University of Medicine and Pharmacy Victor Babes Timisoara	no assertion criteria provided	Pathogenic (Feb 8, 2022)	paternal	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002073733

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

no assertion criteria provided

Pathogenic
(Feb 8, 2022)

paternal

clinical testing

Summary from all submissions

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Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
European	paternal	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, SCV002073733.1

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

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

Last Updated: Apr 23, 2022

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