ClinVar Miner

Submissions for variant NM_018389.5(SLC35C1):c.598G>A (p.Val200Ile)

gnomAD frequency: 0.00118  dbSNP: rs146971634
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000636682 SCV000758122 likely benign Leukocyte adhesion deficiency type II 2024-01-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002528886 SCV003683288 uncertain significance Inborn genetic diseases 2021-07-09 criteria provided, single submitter clinical testing The c.598G>A (p.V200I) alteration is located in exon 2 (coding exon 2) of the SLC35C1 gene. This alteration results from a G to A substitution at nucleotide position 598, causing the valine (V) at amino acid position 200 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Breakthrough Genomics, Breakthrough Genomics RCV001356757 SCV005224236 likely benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356757 SCV001552012 likely benign not provided no assertion criteria provided clinical testing The SLC35C1 p.Val187Ile variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs146971634) and ClinVar (classified as likely benign). The variant was also identified in control databases in 107 of 280140 chromosomes (1 homozygous) at a frequency of 0.000382 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 94 of 24732 chromosomes (freq: 0.003801), Other in 3 of 7176 chromosomes (freq: 0.000418), Latino in 7 of 35384 chromosomes (freq: 0.000198), South Asian in 1 of 30614 chromosomes (freq: 0.000033) and European (non-Finnish) in 2 of 128374 chromosomes (freq: 0.000016), while the variant was not observed in the Ashkenazi Jewish, East Asian, and European (Finnish) populations. The p.Val187 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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