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Variant: NM_005629.4(SLC6A8):c.76G>A (p.Gly26Arg)

CA415076138

643295 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
UUID: 49ff12e7-0969-4d36-a6ca-664d4a65e974
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.76G>A
NM_005629.4(SLC6A8):c.76G>A (p.Gly26Arg)
NC_000023.11:g.153688650G>A
CM000685.2:g.153688650G>A
NC_000023.10:g.152954105G>A
CM000685.1:g.152954105G>A
NC_000023.9:g.152607299G>A
NG_012016.1:g.5354G>A
NG_012016.2:g.5354G>A
ENST00000253122.10:c.76G>A
ENST00000253122.9:c.76G>A
ENST00000458354.5:c.-3+165C>T
ENST00000480693.1:n.64+165C>T
NM_001142805.1:c.76G>A
NM_005629.3:c.76G>A
NM_001142805.2:c.76G>A

Uncertain Significance

Met criteria codes 1
BP4
Not Met criteria codes 3
PS4 PS3 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4(SLC6A8):c.76G>A (p.Gly26Arg) variant in SLC6A8 is a missense variant predicted to cause substitution of Glycine for Arginine at amino acid 26 (p.Gly26Arg). In gnomAD v2.1.1, the highest population minor allele frequency is 0.0000257 (2/77768 alleles) in the European population, and there is 1 hemizygote present in this population database, therefore PM2_Supporting criteria is not met. The computational predictor REVEL gives a score of 0.079 which is below the threshold of 0.25, evidence and does not predict a damaging effect on SLC6A8 function. While functional studies were completed for the SLC6A8 c.76G>A (p.Gly26Arg) (PMID:17465020), they did not meet the specifications required for functional studies by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (<125uM Creatine used for transport assays). This variant has been reported in an individual in the literature (PMID:16738945), however biochemical evidence of Creatine Transport Deficiency (elevated urine creatine:creatinine) was not obtained for this individual, therefore it does not meet criteria established for PP4. There is a ClinVar entry for this variant (Variation ID:655315). 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 0.079 which is below the threshold of 0.25, evidence and does not predict a damaging effect on SLC6A8 function.
Not Met criteria codes
PS4
This variant has been reported in an individual in the literature (PMID:16738945), however biochemical evidence of Creatine Transport Deficiency (elevated urine creatine:creatinine) was not obtained for this individual.
PS3
While functional studies were completed for the SLC6A8 c.76G>A (p.Gly26Arg) (PMID:17465020), they did not meet the the specifications required for functional studies by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (<125uM Creatine used for transport assays; Specifications Version 1.0).
PM2
In gnomAD v2.1.1, the highest population minor allele frequency is 0.0000257 (2/77768 alleles) in the European population, and there is 1 hemizygote present in this population database, therefore PM2_Supporting criteria is not met.
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