chr3-132434209-CAAAAAAA-C

Variant names:

• chr3-132434209-CAAAAAAA-C
• rs544393571
• NM_015268.4:c.-13-323_-13-317delAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015268.4(DNAJC13):​c.-13-323_-13-317delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000931 in 107,446 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000093 (0 hom., cov: 26)
• Consequence: DNAJC13 NM_015268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

DNAJC13 (HGNC:30343): (DnaJ heat shock protein family (Hsp40) member C13) This gene encodes a member of the Dnaj protein family whose members act as co-chaperones of a partner heat-shock protein by binding to the latter and stimulating ATP hydrolysis. The encoded protein associates with the heat-shock protein Hsc70 and plays a role in clathrin-mediated endocytosis. It may also be involved in post-endocytic transport mechanisms via its associations with other proteins, including the sorting nexin SNX1. Mutations in this gene are associated with Parkinson's disease. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAJC13	NM_015268.4	c.-13-323_-13-317delAAAAAAA		intron_variant	Intron 1 of 55	ENST00000260818.11	NP_056083.3
DNAJC13	NM_001329126.2	c.-13-323_-13-317delAAAAAAA		intron_variant	Intron 1 of 56		NP_001316055.1
DNAJC13	XM_047447819.1	c.-13-323_-13-317delAAAAAAA		intron_variant	Intron 1 of 56		XP_047303775.1
DNAJC13	XM_047447820.1	c.-13-323_-13-317delAAAAAAA		intron_variant	Intron 1 of 55		XP_047303776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAJC13	ENST00000260818.11	c.-13-328_-13-322delAAAAAAA		intron_variant	Intron 1 of 55	1	NM_015268.4	ENSP00000260818.6
DNAJC13	ENST00000486798.5	n.53-328_53-322delAAAAAAA		intron_variant	Intron 1 of 19	1
DNAJC13	ENST00000650455.1	n.-13-328_-13-322delAAAAAAA		intron_variant	Intron 1 of 56			ENSP00000496825.1

Frequencies

GnomAD3 genomes AF: 0.00000931 AC: 1 AN: 107446 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000293

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00000931 AC: 1 AN: 107446 Hom.: 0 Cov.: 26 AF XY: 0.0000198 AC XY: 1 AN XY: 50550

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000293

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs544393571; hg19: chr3-132153053;