Is CFAP300 p.Phe14Cys (c.41T>G) pathogenic?

CFAP300 p.Phe14Cys (c.41T>G) is classified Uncertain significance in CFAP300 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-13). AlphaMissense: likely pathogenic (0.8692); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CFAP300 p.Phe14Cys (c.41T>G)?

CFAP300 p.Phe14Cys (c.41T>G) is associated with Inborn genetic diseases (ClinVar).

How common is CFAP300 p.Phe14Cys (c.41T>G) in the general population?

CFAP300 p.Phe14Cys (c.41T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFAP300 p.Phe14Cys (c.41T>G)?

AlphaMissense predicts likely pathogenic (score 0.8692) — an in-silico prediction, not a clinical call.

CFAP300 p.Phe14Cys

c.41T>G · rs1941895921 · VCV3143446

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8692 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8692	likely pathogenic
REVEL	0.579	indeterminate
SaProt	LLR -13.82	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.4, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 36 kb · p 0.034 · regional, not allelic
Overall
CADD	25.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFAP300
Protein: p.Phe14Cys
Coding: c.41T>G
MANE Select: NM_032930
dbSNP: rs1941895921
Type: single nucleotide variant
Location: chr11:102047511 (GRCh38)
Gene constraint: LOEUF 1.386 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.21

Full CFAP300 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP300 p.Phe14Leu Uncertain significance ★ ⚠ same residue
CFAP300 p.Arg252His Uncertain significance ★ ⚠ same condition
CFAP300 p.Glu239Asp Uncertain significance ★ ⚠ same condition
CFAP300 p.Arg121Ter Pathogenic ★★ same type
CFAP300 p.Arg144Ter Pathogenic/Likely pathogenic ★★ same type
CFAP300 p.Gln160Ter Pathogenic ★★ same type
CFAP300 p.Gln52Ter Pathogenic ★★ same type
CFAP300 p.His259Arg Pathogenic/Likely pathogenic ★★ 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/cfap300-p-phe14cys (accessed [today's date]).

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