Is AMT p.Pro25fs (c.74del) pathogenic?

AMT p.Pro25fs (c.74del) is classified Pathogenic in AMT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-03). Absent from gnomAD; Associated with glycine encephalopathy.

What condition is associated with AMT p.Pro25fs (c.74del)?

AMT p.Pro25fs (c.74del) is associated with glycine encephalopathy (ClinVar).

How common is AMT p.Pro25fs (c.74del) in the general population?

AMT p.Pro25fs (c.74del) 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.Pro25fs

c.74del · rs1210592462 · VCV2102638

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	predicted	premature termination codon in exon 1 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.7	GERP -4.4

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.Pro25fs
Coding: c.74del
MANE Select: NM_000481
dbSNP: rs1210592462
Type: Deletion
Location: chr3:49422377 (GRCh38)
Gene constraint: LOEUF 0.805 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.66 · 2 PDB

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.Pro25Ser Uncertain significance ★ ⚠ same residue
AMT p.Pro25= Likely benign ★ same residue
AMT c.471+2_471+7del Likely pathogenic ★★ same condition
AMT c.695_696+21del Likely pathogenic ★★ same condition
AMT p.Gly54_Trp55insTer Pathogenic/Likely pathogenic ★★ same condition
AMT p.His75fs Pathogenic/Likely pathogenic ★★ same condition
AMT p.Leu57fs Pathogenic/Likely pathogenic ★★ same condition
AMT p.Lys201fs Pathogenic/Likely 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/amt-p-pro25fs (accessed [today's date]).

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