Is AFG2B p.Phe360Ser (c.1079T>C) pathogenic?

AFG2B p.Phe360Ser (c.1079T>C) is classified Uncertain significance in AFG2B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-23). AlphaMissense: likely pathogenic (0.9594); Very rare (popmax 8.5e-05%, nfe).

How common is AFG2B p.Phe360Ser (c.1079T>C) in the general population?

AFG2B p.Phe360Ser (c.1079T>C) is very rare (popmax 8.5e-05%, nfe) (gnomAD).

What do computational predictors say about AFG2B p.Phe360Ser (c.1079T>C)?

AlphaMissense predicts likely pathogenic (score 0.9594) — an in-silico prediction, not a clinical call.

AFG2B p.Phe360Ser

c.1079T>C · rs766776373 · VCV1275863

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9594 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.5e-05%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9594	likely pathogenic · top 1% in AFG2B
REVEL	0.945	strongly pathogenic-leaning
SaProt	LLR -15.75	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.7, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 19 kb · p 0.58 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.5e-05% European (non-Finnish) · 1/1,176,220 alleles

Overall 6.89e-05% 1/1,450,670 alleles · very rare

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: AFG2B
Protein: p.Phe360Ser
Coding: c.1079T>C
MANE Select: NM_024063
dbSNP: rs766776373
Type: single nucleotide variant
Location: chr15:45403508 (GRCh38)
Structure: AlphaFold pLDDT 77.37 · 2 PDB
Residue 360: a UniProt-annotated variant site (in nedhls)

Full AFG2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFG2B p.Ile466Met Pathogenic/Likely pathogenic ★★ ⚠ same type
AFG2B p.Thr400Ile Pathogenic/Likely pathogenic ★★ same type
AFG2B p.Arg288Pro Uncertain significance ★★ ⚠ same type
AFG2B p.Arg28Cys Uncertain significance ★★ ⚠ same type
AFG2B p.Phe71Leu Uncertain significance ★★ ⚠ same type
AFG2B p.Pro558Arg Uncertain significance ★★ ⚠ same type
AFG2B p.Ser333Ile Uncertain significance ★★ ⚠ same type
AFG2B p.Tyr738Cys Uncertain significance ★★ ⚠ 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/afg2b-p-phe360ser (accessed [today's date]).

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