Is CFAP20 p.Met121Ile (c.363G>A) pathogenic?

CFAP20 p.Met121Ile (c.363G>A) is classified Uncertain significance in CFAP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-23). AlphaMissense: likely pathogenic (0.9758); Very rare (popmax 0.00322%, nfe).

How common is CFAP20 p.Met121Ile (c.363G>A) in the general population?

CFAP20 p.Met121Ile (c.363G>A) is very rare (popmax 0.00322%, nfe) (gnomAD).

What do computational predictors say about CFAP20 p.Met121Ile (c.363G>A)?

AlphaMissense predicts likely pathogenic (score 0.9758) — an in-silico prediction, not a clinical call.

CFAP20 p.Met121Ile

c.363G>A · VCV3266407

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9758 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00322%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9758	likely pathogenic
REVEL	0.381	indeterminate
SaProt	LLR -13.52	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.6, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 15 kb · p 2.1e-05 · regional, not allelic
Overall
CADD	25.5	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 0.00322% European (non-Finnish) · 38/1,180,056 alleles

Filtering AF 0.00239% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0021%

Overall 0.00248% 40/1,614,108 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00322%	31,054
Remaining individualsnot grpmax-eligible	0.0016%	62,488
Finnishnot grpmax-eligible	0.00156%	64,032

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: CFAP20
Protein: p.Met121Ile
Coding: c.363G>A
MANE Select: NM_013242
Type: single nucleotide variant
Location: chr16:58115371 (GRCh38)
Gene constraint: LOEUF 0.783 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 91.81 · 3 PDB

Full CFAP20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP20 p.Met121Thr Uncertain significance ★ ⚠ same residue
CFAP20 c.164+1G>A Uncertain significance ★ same type
CFAP20 p.Arg101Cys Uncertain significance ★ ⚠ same type
CFAP20 p.Arg113Gln Uncertain significance ★ ⚠ same type
CFAP20 p.Arg113Trp Uncertain significance ★ ⚠ same type
CFAP20 p.Arg161Ser Uncertain significance ★ ⚠ same type
CFAP20 p.Asp39Asn Uncertain significance ★ ⚠ same type
CFAP20 p.Gln92Arg 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/cfap20-p-met121ile (accessed [today's date]).

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