Is GFER p.Arg9fs (c.25del) pathogenic?

GFER p.Arg9fs (c.25del) is classified Uncertain significance in GFER (ClinVar, Single submitter, 1 submitter; last evaluated 2016-10-31). No gnomAD frequency available for this variant.

How common is GFER p.Arg9fs (c.25del) in the general population?

GFER p.Arg9fs (c.25del) is no gnomAD frequency available for this variant (gnomAD).

GFER p.Arg9fs

c.25del · rs1064797204 · VCV425085

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 3
Splicing
SpliceAI	—	not assessed · substitutions only

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: GFER
Protein: p.Arg9fs
Coding: c.25del
MANE Select: NM_005262
dbSNP: rs1064797204
Type: Deletion
Location: chr16:1984242 (GRCh38)
Gene constraint: LOEUF 1.87 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.50 · 7 PDB
Residue 9: the 'disordered' region

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

Similar variants

GFER c.259-25_259-24del Likely pathogenic ★ same type
GFER p.Arg150fs Uncertain significance ★ same type
GFER p.Arg67fs Conflicting classifications of pathogenicity ★ same type
GFER c.-55_-44delGACCTGGAGGCT Likely benign ★ same type

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/gfer-p-arg9fs (accessed [today's date]).

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