9-111649894-CGA-GGG

Variant names:

• chr9-111649894-CGA-GGG
• NM_001015882.3:c.931_933delCGAinsGGG
• DNAJC25 p.Arg311Gly

Variant summary

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

The NM_001015882.3(DNAJC25):​c.931_933delCGAinsGGG​(p.Arg311Gly) variant causes a missense 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 MNV, 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DNAJC25 NM_001015882.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.22
• Publications: 0 publications found

Genes affected

DNAJC25 (HGNC:34187): (DnaJ heat shock protein family (Hsp40) member C25) Predicted to be involved in protein folding. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC25-GNG10 (HGNC:37501): (DNAJC25-GNG10 readthrough) This gene represents naturally-occurring mRNAs that are co-transcribed products of the neighboring DNAJC25 and GNG10 genes. These transcripts include the first exon of DNAJC25 and the last two exons of GNG10, resulting in a protein that combines the N-terminus of DNAJC25 and the C-terminus of GNG10. [provided by RefSeq, Dec 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001015882.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC25	NM_001015882.3	MANE Select	c.931_933delCGAinsGGG	p.Arg311Gly	missense	N/A	NP_001015882.2	Q9H1X3-1
	DNAJC25-GNG10	NM_004125.4		c.337-16921_337-16919delCGAinsGGG		intron	N/A	NP_004116.2
	DNAJC25	NR_037148.2		n.1243_1245delCGAinsGGG		non_coding_transcript_exon	Exon 4 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNAJC25	ENST00000313525.4	TSL:1 MANE Select	c.931_933delCGAinsGGG	p.Arg311Gly	missense	N/A	ENSP00000320650.3	Q9H1X3-1
	DNAJC25-GNG10	ENST00000374294.3	TSL:2	c.337-16921_337-16919delCGAinsGGG		intron	N/A	ENSP00000363412.3
	DNAJC25	ENST00000447096.1	TSL:1	n.*761_*763delCGAinsGGG		non_coding_transcript_exon	Exon 4 of 5	ENSP00000399325.1	F2Z3D1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-114412174;