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Variant: NM_000156.6(GAMT):c.419C>A (p.Ser140Ter)

CA402995274

225369 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: e72bbdd6-26f5-45c3-99b3-e4e9b401ad27
Approved on: 2022-06-06
Published on: 2022-10-07

HGVS expressions

NM_000156.6:c.419C>A
NM_000156.6(GAMT):c.419C>A (p.Ser140Ter)
NC_000019.10:g.1399168G>T
CM000681.2:g.1399168G>T
NC_000019.9:g.1399167G>T
CM000681.1:g.1399167G>T
NC_000019.8:g.1350167G>T
NG_009785.1:g.7386C>A
ENST00000252288.8:c.419C>A
ENST00000447102.8:c.419C>A
ENST00000591788.3:n.102C>A
ENST00000640164.1:n.252C>A
ENST00000640762.1:c.350C>A
ENST00000252288.6:c.419C>A
ENST00000447102.7:c.419C>A
ENST00000591788.2:n.104C>A
NM_000156.5:c.419C>A
NM_138924.2:c.419C>A
NM_138924.3:c.419C>A
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Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 1
BA1

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.419C>A (p.Ser140Ter) variant in GAMT is a nonsense variant that is predicted to cause a premature stop codon in biologically-relevant exon 4/6 that leads to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). To our knowledge, this variant has not been reported in the lietarture in individuals with GAMT deficiency. There is a ClinVar entry for this variant (Variation ID: 225369). The classification of this variant has been upgraded from Variant of Uncertain Significance to Likely Pathogenic based on the recommendations of the ClinGen Sequence Variant Interpretation Working Group, that a variant meeting PVS1 and PM2_Supporting is classified as Likely Pathogenic (https://clinicalgenome.org/site/assets/files/5182/pm2_-_svi_recommendation_-_approved_sept2020.pdf ). GAMT-specific ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PVS1, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
The NM_000156.6:c.419C>A (p.Ser140Ter) variant in GAMT is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 4/6, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1)
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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