Is CFAP20 p.Arg161Ser (c.481C>A) pathogenic?

CFAP20 p.Arg161Ser (c.481C>A) is classified Uncertain significance in CFAP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-27). AlphaMissense: likely pathogenic (0.9914); Very rare (popmax 0.000339%, nfe).

How common is CFAP20 p.Arg161Ser (c.481C>A) in the general population?

CFAP20 p.Arg161Ser (c.481C>A) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about CFAP20 p.Arg161Ser (c.481C>A)?

AlphaMissense predicts likely pathogenic (score 0.9914) — an in-silico prediction, not a clinical call.

CFAP20 p.Arg161Ser

c.481C>A · rs1163431364 · VCV2292595

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9914 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9914	likely pathogenic
REVEL	0.641	indeterminate
SaProt	LLR -15.83	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.24	loss · gain 0.04 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 15 kb · p 2.1e-05 · regional, not allelic
Overall
CADD	34.0	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 0.000339% European (non-Finnish) · 4/1,179,476 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,461,246 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.Arg161Ser
Coding: c.481C>A
MANE Select: NM_013242
dbSNP: rs1163431364
Type: single nucleotide variant
Location: chr16:58114905 (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.Asp39Asn Uncertain significance ★ ⚠ same type
CFAP20 p.Gln92Arg Uncertain significance ★ ⚠ same type
CFAP20 p.Ile49Met Uncertain significance ★ ⚠ same type
CFAP20 p.Leu83Val 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-arg161ser (accessed [today's date]).

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