Is AMT p.Val360fs (c.1079_1080del) pathogenic?

AMT p.Val360fs (c.10791080del) is classified Pathogenic in AMT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-10). Absent from gnomAD; Associated with glycine encephalopathy.

What condition is associated with AMT p.Val360fs (c.1079_1080del)?

AMT p.Val360fs (c.1079_1080del) is associated with glycine encephalopathy (ClinVar).

How common is AMT p.Val360fs (c.1079_1080del) in the general population?

AMT p.Val360fs (c.1079_1080del) is absent from gnomAD (gnomAD).

How is Glycine encephalopathy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AMT p.Val360fs

c.1079_1080del · rs2471145374 · VCV2854597

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

glycine encephalopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (9 of 9) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: AMT
Protein: p.Val360fs
Coding: c.1079_1080del
MANE Select: NM_000481
dbSNP: rs2471145374
Type: Microsatellite
Location: chr3:49417672 (GRCh38)
Gene constraint: LOEUF 0.805 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.66 · 2 PDB
Residue 360: a β-strand

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

Disease context

glycine encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycine encephalopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

AMT p.Met84fs Pathogenic/Likely pathogenic ★★ same condition
AMT p.Gln385del Uncertain significance ★★ same condition
AMT c.471+12_471+13del Benign/Likely benign ★★ same condition
AMT p.Arg73fs Likely pathogenic ★ same condition
AMT p.His333fs Pathogenic ★ same condition
AMT p.Leu356fs Likely pathogenic ★ same condition
AMT p.Ser216fs Pathogenic ★ same condition
AMT p.Lys358del Conflicting classifications of pathogenicity ★ 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/amt-p-val360fs (accessed [today's date]).

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