Is FLNC p.Pro90Thr (c.268C>A) pathogenic?

FLNC p.Pro90Thr (c.268C>A) is classified Uncertain significance in FLNC (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-14). AlphaMissense: likely pathogenic (0.9764); Absent from gnomAD v4.1.

How common is FLNC p.Pro90Thr (c.268C>A) in the general population?

FLNC p.Pro90Thr (c.268C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FLNC p.Pro90Thr (c.268C>A)?

AlphaMissense predicts likely pathogenic (score 0.9764) — an in-silico prediction, not a clinical call.

FLNC p.Pro90Thr

c.268C>A · VCV4975234

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9764 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9764	likely pathogenic
REVEL	0.588	indeterminate
SaProt	LLR -10.35	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 116 bp · p 0.91 · regional, not allelic
Overall
CADD	28.4	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: FLNC
Protein: p.Pro90Thr
Coding: c.268C>A
MANE Select: NM_001458
Type: single nucleotide variant
Location: chr7:128830905 (GRCh38)
Gene constraint: LOEUF 0.424 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 90: the calponin-homology (ch) 1 domain; the 'actin-binding' region

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

Similar variants

FLNC p.Pro90Arg Uncertain significance ★ ⚠ same residue
FLNC p.Pro90= Likely benign ★ same residue
FLNC p.Pro90Ser Likely benign ★ same residue
FLNC c.1047+1G>T Likely pathogenic ★★ same type
FLNC c.1048-1G>A Likely pathogenic ★★ same type
FLNC c.1210+1G>A Likely pathogenic ★★ same type
FLNC c.1549+2T>G Likely pathogenic ★★ same type
FLNC c.2007+1G>A 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/flnc-p-pro90thr (accessed [today's date]).

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