ENST00000238018.8:c.1399_1401delCCTinsTCG

Variant names:

• chr9-72250787-CCT-TCG
• ENST00000238018.8:c.1399_1401delCCTinsTCG
• GDA p.Pro467Ser

Variant summary

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

The ENST00000238018.8(GDA):​c.1399_1401delCCTinsTCG​(p.Pro467Ser) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GDA ENST00000238018.8 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 0 publications found

Genes affected

GDA (HGNC:4212): (guanine deaminase) This gene encodes an enzyme responsible for the hydrolytic deamination of guanine. Studies in rat ortholog suggest this gene plays a role in microtubule assembly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000238018.8. 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
	GDA	NM_004293.5	MANE Select	c.*2445_*2447delCCTinsTCG		3_prime_UTR	Exon 14 of 14	NP_004284.1	Q9Y2T3-1
	GDA	NM_001242505.3		c.1399_1401delCCTinsTCG	p.Pro467Ser	missense	N/A	NP_001229434.1	Q9Y2T3-3
	GDA	NM_001351572.2		c.1399_1401delCCTinsTCG	p.Pro467Ser	missense	N/A	NP_001338501.1	Q9Y2T3-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDA	ENST00000238018.8	TSL:1	c.1399_1401delCCTinsTCG	p.Pro467Ser	missense	N/A	ENSP00000238018.4	Q9Y2T3-3
	GDA	ENST00000358399.8	TSL:1 MANE Select	c.*2445_*2447delCCTinsTCG		3_prime_UTR	Exon 14 of 14	ENSP00000351170.4	Q9Y2T3-1
	GDA	ENST00000475764.5	TSL:1	n.*102_*104delCCTinsTCG		non_coding_transcript_exon	Exon 15 of 16	ENSP00000436619.1	Q9Y2T3-1

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		-0.20

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: chr9-74865703;