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Variant: NM_000156.6(GAMT):c.677C>T (p.Pro226Leu)

CA314832

205594 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 1321fc98-d624-47f8-847a-0e4462c166b0
Approved on: 2022-06-06
Published on: 2022-10-07

HGVS expressions

NM_000156.6:c.677C>T
NM_000156.6(GAMT):c.677C>T (p.Pro226Leu)
NC_000019.10:g.1397393G>A
CM000681.2:g.1397393G>A
NC_000019.9:g.1397392G>A
CM000681.1:g.1397392G>A
NC_000019.8:g.1348392G>A
NG_008283.1:g.18510G>A
NG_009785.1:g.9161C>T
ENST00000252288.8:c.677C>T
ENST00000640164.1:n.510C>T
ENST00000640762.1:c.608C>T
ENST00000252288.6:c.677C>T
NM_000156.5:c.677C>T

Uncertain Significance

Met criteria codes 2
BP4 PM2_Supporting

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 GAMT Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6: c.677C>T variant in GAMT is a missense variant predicted to result in the substitution of proline for leucine at amino acid 226 (p.Pro226Leu). It is absent in gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.292 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAMT function (BP4). To our knowledge, this variant has not been reported in published literature in individuals with GAMT deficiency, and the results of functional studies are unavailable. This variant has been previously reported in ClinVar (Variation ID: 205594). In summary, this variant meets the criteria to be classified as a variant of uncertain significancefor GAMT deficiency. GAMT-specific ACMG/AMP codes met, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes VCEP (Specifications Version 1.1.0): PM2_Supporting, BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.292 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAMT function (BP4).
PM2_Supporting
It is absent in gnomAD v2.1.1 (PM2_Supporting).
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