The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_005629.4(SLC6A8):c.912G>C (p.Gln304His)

CA16621223

420991 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 69259e89-7458-4e02-8714-267be869a20c

HGVS expressions

NM_005629.4:c.912G>C
NM_005629.4(SLC6A8):c.912G>C (p.Gln304His)
NC_000023.11:g.153693175G>C
CM000685.2:g.153693175G>C
NC_000023.10:g.152958630G>C
CM000685.1:g.152958630G>C
NC_000023.9:g.152611824G>C
NG_012016.1:g.9879G>C
NG_012016.2:g.9879G>C
ENST00000253122.10:c.912G>C
ENST00000253122.9:c.912G>C
ENST00000413787.1:c.122G>C
ENST00000430077.6:c.567G>C
ENST00000467402.1:n.146-317G>C
ENST00000485324.1:n.945G>C
NM_001142805.1:c.912G>C
NM_001142806.1:c.567G>C
NM_005629.3:c.912G>C
NM_001142805.2:c.912G>C

Uncertain Significance

Met criteria codes 3
PS1_Supporting PM2_Supporting PP3
Not Met criteria codes 1
PS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4:c.912G>C in SLC6A8 is a missense variant predicted to cause substitution of glutamine by histidine at amino acid 304 (p.Gln304His). The variant is absent in gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.749 (>0.75 provides evidence that correlates with impact to SLC6A8 function). The computational splicing predictors SpliceAI and varSEAK predict that the variant may disrupt the donor splice site of intron 5 (PP3). Another variant at this position, c.912G>A (p.Gln304=), which has been reported in a patient with creatine transporter deficiency and may disrupt normal splicing of SLC6A8 (PMIDs: 17101918, 23660394, 29478817) has been classified as likely pathogenic by the ClinGen CCDS VCEP. Comparison of the in silico predictions for c.912G>A (p.Gln304=) and c.912G>C (p.Gln304His) suggest that c.912G>A (p.Gln304=) is less damaging to splicing than c.912G>C (p.Gln304His) (PS1_Supporting). To our knowledge, c.912G>C (p.Gln304His) has not been reported in the literature and results of functional and splicing studies are unavailable. However, there is a ClinVar entry for this variant (Variation ID: 420991); follow up with the lab did not provide sufficient evidence to apply additional criteria. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for X-linked creatine transporter deficiency. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): PP3, PM2_Supporting, PS1_Supporting. (Classification approved by the ClinGen CCDS VCEP, Jan 12, 2023)
Met criteria codes
PS1_Supporting
Another variant at this codon, c.912G>A (p.Gln304=) has been reported in a patient with creatine transporter deficiency and may disrupt normal splicing of SLC6A8 (PMIDs: 17101918, 23660394, 29478817). Comparison of the in silico predictions for c.912G>A and c.912G>C suggest that c.912G>A is less damaging to splicing than c.912G>C (SpliceAI score 0.54 vs 0.78, and varSEAK class 4 "likely splicing effect" vs Class 5 "splicing effect". Therefore PS1_Supporting is applied, consistent with ACGS recommendations (https://www.acgs.uk.com/media/11631/uk-practice-guidelines-for-variant-classification-v4-01-2020.pdf).
PM2_Supporting
This variant is not in gnomAD v2.1.1 (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.749. The threshold of >0.75 provides evidence that correlates with impact to SLC6A8 function. Of note, the variant alters the last nucleotide of exon 5. The computational splicing predictors SpliceAI and varSEAK both predict that the variant may disrupt the donor splice site of intron 5. SpliceAI gives a score of 0.78 for donor loss, and varSEAK gives a prediction of Class 5 (i.e. "splicing effect) with "Loss of function for authentic Splice Site" (PP3).
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-08-24
Published on: 2023-08-24
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