GeneBe

rs563818595

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_025219.3(DNAJC5):​c.-178_-161delCTGCCGCTGCCGCTGCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DNAJC5
NM_025219.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.63

Publications

0 publications found
Variant links:
Genes affected
DNAJC5 (HGNC:16235): (DnaJ heat shock protein family (Hsp40) member C5) This gene is a member of the J protein family. J proteins function in many cellular processes by regulating the ATPase activity of 70 kDa heat shock proteins. The encoded protein plays a role in membrane trafficking and protein folding, and has been shown to have anti-neurodegenerative properties. The encoded protein is known to play a role in cystic fibrosis and Huntington's disease. A pseudogene of this gene is located on the short arm of chromosome 8. [provided by RefSeq, Nov 2010]
DNAJC5 Gene-Disease associations (from GenCC):
  • ceroid lipofuscinosis, neuronal, 4 (Kufs type)
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
  • adult neuronal ceroid lipofuscinosis
    Inheritance: AD Classification: MODERATE Submitted by: ClinGen

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025219.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DNAJC5
NM_025219.3
MANE Select
c.-178_-161delCTGCCGCTGCCGCTGCCG
5_prime_UTR
Exon 1 of 5NP_079495.1Q9H3Z4-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DNAJC5
ENST00000360864.9
TSL:1 MANE Select
c.-178_-161delCTGCCGCTGCCGCTGCCG
5_prime_UTR
Exon 1 of 5ENSP00000354111.4Q9H3Z4-1
DNAJC5
ENST00000898575.1
c.-173_-156delCTGCCGCTGCCGCTGCCG
5_prime_UTR
Exon 1 of 5ENSP00000568634.1
DNAJC5
ENST00000921989.1
c.-90_-73delCTGCCGCTGCCGCTGCCG
5_prime_UTR
Exon 1 of 5ENSP00000592048.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2982
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2038
African (AFR)
AF:
0.00
AC:
0
AN:
26
American (AMR)
AF:
0.00
AC:
0
AN:
26
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14
East Asian (EAS)
AF:
0.00
AC:
0
AN:
122
South Asian (SAS)
AF:
0.00
AC:
0
AN:
880
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
6
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1788
Other (OTH)
AF:
0.00
AC:
0
AN:
92
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs563818595; hg19: chr20-62526500; API