Is AMER1 p.Gln232fs (c.694del) pathogenic?

AMER1 p.Gln232fs (c.694del) is classified Pathogenic in AMER1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-09). Associated with osteopathia striata with cranial sclerosis.

What condition is associated with AMER1 p.Gln232fs (c.694del)?

AMER1 p.Gln232fs (c.694del) is associated with osteopathia striata with cranial sclerosis (ClinVar).

AMER1 p.Gln232fs

c.694del · VCV3377319

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

osteopathia striata with cranial sclerosis

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 (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.98	GERP -2.7, phastCons 0.73

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

Variant & gene context

Gene: AMER1
Protein: p.Gln232fs
Coding: c.694del
MANE Select: NM_152424
Type: Deletion
Location: chrX:64192593 (GRCh38)
Structure: AlphaFold pLDDT 48.88 · 3 PDB
Residue 232: the 'disordered' region

Full AMER1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

osteopathia striata with cranial sclerosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AMER1 p.Glu462fs Likely pathogenic ★ same condition
AMER1 p.Gly186_Ala187insTer Pathogenic ★ same condition
AMER1 p.His104fs Pathogenic ★ same condition
AMER1 p.Lys292_Val293insTer Pathogenic ★ same condition
AMER1 p.Phe60fs Pathogenic ★ same condition
AMER1 p.Tyr526fs Likely pathogenic ★ same condition
AMER1 p.Glu219fs Likely pathogenic same condition
AMER1 p.Leu423fs 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/amer1-p-gln232fs (accessed [today's date]).

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