Is CFAP20 p.Val54Ile (c.160G>A) pathogenic?

CFAP20 p.Val54Ile (c.160G>A) is classified Uncertain significance in CFAP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-19). AlphaMissense: likely benign (0.2086); Very rare (popmax 0.005%, amr).

How common is CFAP20 p.Val54Ile (c.160G>A) in the general population?

CFAP20 p.Val54Ile (c.160G>A) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about CFAP20 p.Val54Ile (c.160G>A)?

AlphaMissense predicts likely benign (score 0.2086) — an in-silico prediction, not a clinical call.

CFAP20 p.Val54Ile

c.160G>A · VCV3491210

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2086 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2086	likely benign
REVEL	0.099	moderately benign-leaning
SaProt	LLR -12.67	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.4, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 15 kb · p 2.1e-05 · regional, not allelic
Overall
CADD	22.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,012 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000205% 3/1,461,642 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: CFAP20
Protein: p.Val54Ile
Coding: c.160G>A
MANE Select: NM_013242
Type: single nucleotide variant
Location: chr16:58116876 (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 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
CFAP20 p.Ile49Met 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-val54ile (accessed [today's date]).

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