Is CD14 p.Phe69Cys (c.206T>G) pathogenic?

CD14 p.Phe69Cys (c.206T>G) is classified Uncertain significance in CD14 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-23). AlphaMissense: likely pathogenic (0.8522); Absent from gnomAD v4.1.

How common is CD14 p.Phe69Cys (c.206T>G) in the general population?

CD14 p.Phe69Cys (c.206T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD14 p.Phe69Cys (c.206T>G)?

AlphaMissense predicts likely pathogenic (score 0.8522) — an in-silico prediction, not a clinical call.

CD14 p.Phe69Cys

c.206T>G · rs2481046794 · VCV2478031

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8522 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8522	likely pathogenic · top 5% in CD14
REVEL	0.435	indeterminate
SaProt	LLR -10.68	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 7.9	GERP 2, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 1,212 bp · p 0.37 · regional, not allelic
Overall
CADD	23.7	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: CD14
Protein: p.Phe69Cys
Coding: c.206T>G
MANE Select: NM_000591
dbSNP: rs2481046794
Type: single nucleotide variant
Location: chr5:140632778 (GRCh38)
Gene constraint: LOEUF 1.944 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.36 · 1 PDB

Full CD14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD14 p.Ala114Thr Uncertain significance ★ ⚠ same type
CD14 p.Ala143Gly Uncertain significance ★ ⚠ same type
CD14 p.Ala184Thr Uncertain significance ★ ⚠ same type
CD14 p.Ala269Thr Uncertain significance ★ ⚠ same type
CD14 p.Ala75Gly Uncertain significance ★ ⚠ same type
CD14 p.Ala98Ser Uncertain significance ★ ⚠ same type
CD14 p.Arg111His Uncertain significance ★ ⚠ same type
CD14 p.Arg117Ser 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/cd14-p-phe69cys (accessed [today's date]).

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