Is GAMT p.Ser2= (c.6C>T) pathogenic?

GAMT p.Ser2= (c.6C>T) is classified Likely benign in GAMT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-15). No allele count reported in gnomAD v4.1 (AN 1,359,444); Associated with cerebral creatine deficiency syndrome.

What condition is associated with GAMT p.Ser2= (c.6C>T)?

GAMT p.Ser2= (c.6C>T) is associated with cerebral creatine deficiency syndrome (ClinVar).

How common is GAMT p.Ser2= (c.6C>T) in the general population?

GAMT p.Ser2= (c.6C>T) is no allele count reported in gnomAD v4.1 (AN 1,359,444) (gnomAD).

GAMT p.Ser2=

c.6C>T · rs2512229362 · VCV2035678

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,359,444)

Conditions

cerebral creatine deficiency syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.67	GERP -2.3, phastCons 0.61
Overall
CADD	11.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,359,444). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GAMT
Protein: p.Ser2=
Coding: c.6C>T
MANE Select: NM_000156
dbSNP: rs2512229362
Type: single nucleotide variant
Location: chr19:1401471 (GRCh38)
Gene constraint: LOEUF 1.536 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.73 · 1 PDB
Residue 2: a modified residue (n-acetylserine)

Full GAMT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cerebral creatine deficiency syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GAMT c.328-1G>A Pathogenic ★★★ same condition
GAMT c.328-2A>G Pathogenic ★★★ same condition
GAMT c.391+15G>T Likely pathogenic ★★★ same condition
GAMT c.391+1G>C Pathogenic ★★★ same condition
GAMT c.391+5G>C Likely pathogenic ★★★ same condition
GAMT p.Ala156Asp Likely pathogenic ★★★ same condition
GAMT p.Ala74Pro Likely pathogenic ★★★ same condition
GAMT p.Ala75Val Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gamt-p-ser2 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown