Is CFAP144 p.Pro102Ala (c.304C>G) pathogenic?

CFAP144 p.Pro102Ala (c.304C>G) is classified Uncertain significance in CFAP144 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-24). AlphaMissense: likely benign (0.1093); Very rare (popmax 8.48e-05%, nfe).

How common is CFAP144 p.Pro102Ala (c.304C>G) in the general population?

CFAP144 p.Pro102Ala (c.304C>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about CFAP144 p.Pro102Ala (c.304C>G)?

AlphaMissense predicts likely benign (score 0.1093) — an in-silico prediction, not a clinical call.

CFAP144 p.Pro102Ala

c.304C>G · VCV3491172

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1093 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1093	likely benign
REVEL	0.081	moderately benign-leaning
SaProt	LLR -7.74	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 0.85, phastCons 0.097
Regional constraint	o/e 0.91	unconstrained · MANE · 8,358 bp · p 0.24 · regional, not allelic
Overall
CADD	17.18	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 8.48e-05% European (non-Finnish) · 1/1,179,812 alleles

Overall 6.84e-05% 1/1,461,630 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: CFAP144
Protein: p.Pro102Ala
Coding: c.304C>G
MANE Select: NM_001101376
Type: single nucleotide variant
Location: chr1:43156212 (GRCh38)
Structure: AlphaFold pLDDT 79.41 · 2 PDB

Full CFAP144 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP144 p.Arg104Cys Uncertain significance ★ ⚠ same type
CFAP144 p.Asp130Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp57Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp64Asn Uncertain significance ★ ⚠ same type
CFAP144 p.Glu60Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Gly129Val Uncertain significance ★ ⚠ same type
CFAP144 p.His56Tyr Uncertain significance ★ ⚠ same type
CFAP144 p.Ile100Val Conflicting classifications of pathogenicity ★ ⚠ 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/cfap144-p-pro102ala (accessed [today's date]).

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