Is FLG p.Ser555Pro (c.1663T>C) pathogenic?

FLG p.Ser555Pro (c.1663T>C) is classified Uncertain significance in FLG (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-02). AlphaMissense: likely benign (0.227); Rare (popmax 0.113%, afr); Associated with Inborn genetic diseases.

What condition is associated with FLG p.Ser555Pro (c.1663T>C)?

FLG p.Ser555Pro (c.1663T>C) is associated with Inborn genetic diseases (ClinVar).

How common is FLG p.Ser555Pro (c.1663T>C) in the general population?

FLG p.Ser555Pro (c.1663T>C) is rare (popmax 0.113%, afr) (gnomAD).

What do computational predictors say about FLG p.Ser555Pro (c.1663T>C)?

AlphaMissense predicts likely benign (score 0.227) — an in-silico prediction, not a clinical call.

FLG p.Ser555Pro

c.1663T>C · rs775615102 · VCV2342262

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.227 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.113%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.227	likely benign
REVEL	0.042	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.3	GERP -2.2
Regional constraint	o/e 1.77	unconstrained · MANE · 8,404 bp · p 0 · regional, not allelic
Overall
CADD	12.99	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 is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.113% African / African-American · 84/74,630 alleles

Filtering AF 0.0931% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0859%

Overall 0.0057% 92/1,613,514 alleles · rare exomes 36/1,461,892 · genomes 56/151,622 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.113%	888
Remaining individualsnot grpmax-eligible	0.008%	12,495
Admixed American	0.005%	19,989

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: FLG
Protein: p.Ser555Pro
Coding: c.1663T>C
MANE Select: NM_002016
dbSNP: rs775615102
Type: single nucleotide variant
Location: chr1:152313223 (GRCh38)

Full FLG 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

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/flg-p-ser555pro (accessed [today's date]).

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