Is GFER p.Ter206= (c.617AG[3]) pathogenic?

GFER p.Ter206= (c.617AG[3]) is classified Likely benign in GFER (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-22). Ultra-rare (popmax 0.0972%, afr).

How common is GFER p.Ter206= (c.617AG[3]) in the general population?

GFER p.Ter206= (c.617AG[3]) is ultra-rare (popmax 0.0972%, afr) (gnomAD).

GFER p.Ter206=

c.617AG[3] · rs776890492 · VCV1301014

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

stop-loss

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0972%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	stop-loss	predicted loss-of-function
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.2	GERP 1.6, phastCons 1
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0972% African / African-American · 73/75,066 alleles

Filtering AF 0.0793% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0727%

Overall 0.00558% 90/1,612,498 alleles · ultra-rare exomes 52/1,460,160 · genomes 38/152,338 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0972%	1,028
Admixed American	0.015%	6,669
Remaining individualsnot grpmax-eligible	0.0128%	7,811

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GFER
Protein: p.Ter206=
Coding: c.617AG[3]
MANE Select: NM_005262
dbSNP: rs776890492
Type: Microsatellite
Location: chr16:1986026 (GRCh38)
Gene constraint: LOEUF 1.87 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.50 · 7 PDB

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

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-ter206 (accessed [today's date]).

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