Variant chrX-48904529-TCACCCTACCAGGAAGGGTTCACGTGACACCCAGCTCTAGTCCCACACCCCTCCAGAAGTCTCAGTGACCTGGGAGAAAAGACCATCTCCCAAACCCAGAGGAGCCAGGCCCCGGAGGGTGGCGACTTGGGTCCTGCAGATGCCCAACACCCTCCACCCCAGTCCCCCTCCCTTGTGTCCCCCCATTGCTGCCAGCCCTCACTTCACCAGCACTGACTTTGGCAGAAAGGGCTCCGTGATGAGGTCTCCACGGTGGGAAGACAGCTGCGGTGGTGGTGGCTGCCC-CCTCCCG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2

The NM_005660.3(SLC35A2):c.1096_1163+217delinsCGGGAGG variant causes a splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

SLC35A2
NM_005660.3 splice_donor, splice_donor_5th_base, coding_sequence, intron

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.10

Variant links:

Genes affected

SLC35A2 (HGNC:11022): (solute carrier family 35 member A2) This gene encodes a member of the nucleotide-sugar transporter family. The encoded protein is a multi-pass membrane protein. It transports UDP-galactose from the cytosol into Golgi vesicles, where it serves as a glycosyl donor for the generation of glycans. Mutations in this gene cause congenital disorder of glycosylation type IIm (CDG2M). Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Oct 2014]

SLC35A2 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates 0.07976490344248532 fraction of the geneNo cryptic splice site detected. Exon removal results in frameshift change.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A2	NM_005660.3 linkuse as main transcript	c.1096_1163+217delinsCGGGAGG		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	4/5	ENST00000247138.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A2	ENST00000247138.11 linkuse as main transcript	c.1096_1163+217delinsCGGGAGG		splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	4/5	1	NM_005660.3	P1	P78381-1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Sep 21, 2024

Frameshift variant predicted to result in abnormal protein length as the last 28 amino acid(s) are replaced with 10 different amino acid(s); Not observed in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.