Is CFAP73 p.Ala186Ser (c.556G>T) pathogenic?

CFAP73 p.Ala186Ser (c.556G>T) is classified Uncertain significance in CFAP73 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-24). AlphaMissense: likely benign (0.123); Absent from gnomAD v4.1.

How common is CFAP73 p.Ala186Ser (c.556G>T) in the general population?

CFAP73 p.Ala186Ser (c.556G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFAP73 p.Ala186Ser (c.556G>T)?

AlphaMissense predicts likely benign (score 0.123) — an in-silico prediction, not a clinical call.

CFAP73 p.Ala186Ser

c.556G>T · VCV3832423

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.123 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,534,594)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.123	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -8.16	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 1.7	GERP -0.015, phastCons 0.004
Regional constraint	o/e 0.95	unconstrained · MANE · 7,818 bp · p 0.33 · regional, not allelic
Overall
CADD	12.92	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

No allele count reported in gnomAD v4.1 (AN 1,534,594). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CFAP73
Protein: p.Ala186Ser
Coding: c.556G>T
MANE Select: NM_001144872
Type: single nucleotide variant
Location: chr12:113154501 (GRCh38)
Gene constraint: LOEUF 1.354 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.57 · 1 PDB

Full CFAP73 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX54 p.Gly875Asp Uncertain significance ★★ ⚠ same type
CFAP73 p.Ala103Val Uncertain significance ★ ⚠ same type
CFAP73 p.Ala109Gly Uncertain significance ★ ⚠ same type
CFAP73 p.Ala150Glu Uncertain significance ★ ⚠ same type
CFAP73 p.Ala171Thr Uncertain significance ★ ⚠ same type
CFAP73 p.Ala175Val Uncertain significance ★ ⚠ same type
CFAP73 p.Ala214Thr Uncertain significance ★ ⚠ same type
CFAP73 p.Arg106Lys 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/cfap73-p-ala186ser (accessed [today's date]).

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