chr9-96321332-CCC-GCG

Variant names:

• chr9-96321332-CCC-GCG
• NM_007001.3:c.922_924delGGGinsCGC
• SLC35D2 p.Gly308Arg

Variant summary

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

The NM_007001.3(SLC35D2):​c.922_924delGGGinsCGC​(p.Gly308Arg) variant causes a missense change. 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: SLC35D2 NM_007001.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63
• Publications: 0 publications found

Genes affected

SLC35D2 (HGNC:20799): (solute carrier family 35 member D2) Nucleotide sugars, which are synthesized in the cytosol or the nucleus, are high-energy donor substrates for glycosyltransferases located in the lumen of the endoplasmic reticulum and Golgi apparatus. Translocation of nucleotide sugars from the cytosol into the lumen compartment is mediated by specific nucleotide sugar transporters, such as SLC35D2 (Suda et al., 2004 [PubMed 15082721]).[supplied by OMIM, Mar 2008]

ENSG00000285269 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007001.3. 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
	SLC35D2	NM_007001.3	MANE Select	c.922_924delGGGinsCGC	p.Gly308Arg	missense	N/A	NP_008932.2	Q76EJ3-1
	SLC35D2	NM_001286990.2		c.658_660delGGGinsCGC	p.Gly220Arg	missense	N/A	NP_001273919.1	Q76EJ3-2
	SLC35D2	NR_104627.2		n.999_1001delGGGinsCGC		non_coding_transcript_exon	Exon 12 of 13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35D2	ENST00000253270.13	TSL:1 MANE Select	c.922_924delGGGinsCGC	p.Gly308Arg	missense	N/A	ENSP00000253270.7	Q76EJ3-1
	SLC35D2	ENST00000375259.9	TSL:1	c.658_660delGGGinsCGC	p.Gly220Arg	missense	N/A	ENSP00000364408.4	Q76EJ3-2
	ENSG00000285269	ENST00000643789.1		n.523_525delGGGinsCGC		non_coding_transcript_exon	Exon 8 of 22	ENSP00000494818.1	A0A2R8Y5X9

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		4.6

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: chr9-99083614;