Is CFAP119 p.Phe124Leu (c.370T>C) pathogenic?

CFAP119 p.Phe124Leu (c.370T>C) is classified Uncertain significance in CFAP119 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-09). AlphaMissense: likely pathogenic (0.8945); Absent from gnomAD v4.1.

How common is CFAP119 p.Phe124Leu (c.370T>C) in the general population?

CFAP119 p.Phe124Leu (c.370T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFAP119 p.Phe124Leu (c.370T>C)?

AlphaMissense predicts likely pathogenic (score 0.8945) — an in-silico prediction, not a clinical call.

CFAP119 p.Phe124Leu

c.370T>C · rs2053673337 · VCV3143305

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8945 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8945	likely pathogenic · top 5% in CFAP119
REVEL	0.326	indeterminate
SaProt	LLR -6.17	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.1	GERP 2.2, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 4,269 bp · p 0.72 · regional, not allelic
Overall
CADD	23.8	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

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: CFAP119
Protein: p.Phe124Leu
Coding: c.370T>C
MANE Select: NM_001014979
dbSNP: rs2053673337
Type: single nucleotide variant
Location: chr16:30760383 (GRCh38)
Structure: AlphaFold pLDDT 74.17

Full CFAP119 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP119 p.Ala118Thr Uncertain significance ★ ⚠ same type
CFAP119 p.Ala127Thr Uncertain significance ★ ⚠ same type
CFAP119 p.Ala143Val Uncertain significance ★ ⚠ same type
CFAP119 p.Ala196Ser Uncertain significance ★ ⚠ same type
CFAP119 p.Ala196Val Uncertain significance ★ ⚠ same type
CFAP119 p.Ala53Val Uncertain significance ★ ⚠ same type
CFAP119 p.Arg132Cys Uncertain significance ★ ⚠ same type
CFAP119 p.Arg181Trp 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/cfap119-p-phe124leu (accessed [today's date]).

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