Is CFAP161 p.Arg203His (c.608G>A) pathogenic?

CFAP161 p.Arg203His (c.608G>A) is classified Uncertain significance in CFAP161 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-23). AlphaMissense: ambiguous (0.3913); Rare (popmax 0.124%, afr).

How common is CFAP161 p.Arg203His (c.608G>A) in the general population?

CFAP161 p.Arg203His (c.608G>A) is rare (popmax 0.124%, afr) (gnomAD).

What do computational predictors say about CFAP161 p.Arg203His (c.608G>A)?

AlphaMissense predicts ambiguous (score 0.3913) — an in-silico prediction, not a clinical call.

CFAP161 p.Arg203His

c.608G>A · rs201412100 · VCV3143343

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3913 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.124%, afr)

Computational evidence

Protein change
AlphaMissense	0.3913	ambiguous
REVEL	0.481	indeterminate
SaProt	LLR -13.12	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 14 kb · p 0.8 · regional, not allelic
Overall
CADD	27.4	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 0.124% African / African-American · 93/75,026 alleles

Filtering AF 0.104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.096%

Overall 0.00861% 139/1,614,058 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.124%	807
East Asian	0.0446%	2,244
Middle Eastern	0.033%	3,029
Admixed American	0.0233%	4,287
Remaining individualsnot grpmax-eligible	0.0096%	10,417
European (non-Finnish)	0.000339%	294,997

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: CFAP161
Protein: p.Arg203His
Coding: c.608G>A
MANE Select: NM_173528
dbSNP: rs201412100
Type: single nucleotide variant
Location: chr15:81143792 (GRCh38)
Gene constraint: LOEUF 1.029 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.29 · 2 PDB

Full CFAP161 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP161 p.Arg203Cys Uncertain significance ★ ⚠ same residue
CFAP161 p.Ala115Thr Uncertain significance ★ ⚠ same type
CFAP161 p.Ala295Ser Uncertain significance ★ ⚠ same type
CFAP161 p.Ala2Ser Uncertain significance ★ ⚠ same type
CFAP161 p.Arg226Gln Uncertain significance ★ ⚠ same type
CFAP161 p.Arg226Trp Uncertain significance ★ ⚠ same type
CFAP161 p.Arg87His Uncertain significance ★ ⚠ same type
CFAP161 p.Asn14Lys 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/cfap161-p-arg203his (accessed [today's date]).

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