Is CFAP206 p.Arg601Cys (c.1801C>T) pathogenic?

CFAP206 p.Arg601Cys (c.1801C>T) is classified Uncertain significance in CFAP206 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-10). AlphaMissense: likely benign (0.1744); Ultra-rare (popmax 0.0928%, nfe).

How common is CFAP206 p.Arg601Cys (c.1801C>T) in the general population?

CFAP206 p.Arg601Cys (c.1801C>T) is ultra-rare (popmax 0.0928%, nfe) (gnomAD).

What do computational predictors say about CFAP206 p.Arg601Cys (c.1801C>T)?

AlphaMissense predicts likely benign (score 0.1744) — an in-silico prediction, not a clinical call.

CFAP206 p.Arg601Cys

c.1801C>T · rs146571078 · VCV2249836

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1744 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0928%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1744	likely benign
REVEL	0.451	indeterminate
SaProt	LLR -6.12	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 1.6, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 54 kb · p 0.001 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.0928% European (non-Finnish) · 1,095/1,179,996 alleles

Filtering AF 0.0882% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0864%

Overall 0.0725% 1,170/1,614,072 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0928%	1,078
Remaining individualsnot grpmax-eligible	0.0352%	2,841
South Asian	0.034%	2,938
Admixed American	0.0167%	6,000
Middle Eastern	0.0165%	6,062
African / African-American	0.012%	8,336
East Asian	0.00223%	44,878
Finnishnot grpmax-eligible	0.00156%	64,018

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: CFAP206
Protein: p.Arg601Cys
Coding: c.1801C>T
MANE Select: NM_001031743
dbSNP: rs146571078
Type: single nucleotide variant
Location: chr6:87464182 (GRCh38)
Gene constraint: LOEUF 0.992 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.41

Full CFAP206 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP206 p.Ala121Ser Uncertain significance ★ ⚠ same type
CFAP206 p.Ala213Val Uncertain significance ★ ⚠ same type
CFAP206 p.Ala255Thr Uncertain significance ★ ⚠ same type
CFAP206 p.Ala265Glu Uncertain significance ★ ⚠ same type
CFAP206 p.Ala265Val Uncertain significance ★ ⚠ same type
CFAP206 p.Ala393Val Uncertain significance ★ ⚠ same type
CFAP206 p.Arg114Gln Uncertain significance ★ ⚠ same type
CFAP206 p.Arg132Trp 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/cfap206-p-arg601cys (accessed [today's date]).

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