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Variant: NM_005629.4(SLC6A8):c.89C>T (p.Ala30Val)

CA10549150

650071 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: dae0c36e-2df9-4025-bfa0-4352e2770d82
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.89C>T
NM_005629.4(SLC6A8):c.89C>T (p.Ala30Val)
NC_000023.11:g.153688663C>T
CM000685.2:g.153688663C>T
NC_000023.10:g.152954118C>T
CM000685.1:g.152954118C>T
NC_000023.9:g.152607312C>T
NG_012016.1:g.5367C>T
NG_012016.2:g.5367C>T
ENST00000253122.10:c.89C>T
ENST00000253122.9:c.89C>T
ENST00000458354.5:c.-3+152G>A
ENST00000480693.1:n.64+152G>A
NM_001142805.1:c.89C>T
NM_005629.3:c.89C>T
NM_001142805.2:c.89C>T

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 1
PM2

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4(SLC6A8):c.89C>T (p.Ala30Val) variant in SLC6A8 is a missense variant predicted to cause substitution of Alanine for Valine at amino acid 30 (p.Ala30Val). In gnomAD v2.1.1, the highest population minor allele frequency is 0.001205 (1/830 alleles) in the European population with 1 hemizygote, which is <0.0002 and >1 hemizygote, therefore PM2_Supporting criteria is not applicable. The computational predictor REVEL gives a score of 0.096 which is below the threshold of 0.25, and does not predict a damaging effect on SLC6A8 function, and SpliceAI predicts no impact on splicing (BP4). This variant has not been previously reported in affected individuals in the literature. There is a ClinVar entry for this variant (Variation ID:650071). In summary, this variant meets the criteria to be classified as a Variant of Uncertain Significance for Creatine Transporter Deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.096 which is below the threshold of 0.25, and does not predict a damaging effect on SLC6A8 function, and SpliceAI predicts no impact on splicing.
Not Met criteria codes
PM2
In gnomAD v2.1.1, the highest population minor allele frequency is 0.001205 (1/830 alleles) in the European population with 1 hemizygote, which is <0.0002 and >1 hemizygote, therefore PM2_Supporting criteria is not applicable.
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