Is FLG2 p.Ala1602= (c.4806C>T) pathogenic?

FLG2 p.Ala1602= (c.4806C>T) is classified Benign in FLG2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-05-04). Common (popmax 19.9%, afr) — too common for a highly-penetrant pathogenic allele.

FLG2 p.Ala1602=

Q: How common is FLG2 p.Ala1602= (c.4806C>T) in the general population?

FLG2 p.Ala1602= (c.4806C>T) is common (popmax 19.9%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.4806C>T · rs73007787 · VCV1235951

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 19.9%, afr) — too common for a highly-penetrant pathogenic allele

⚠ 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
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not looked up on this page · why
Overall
CADD	2.066	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 19.9% African / African-American · 14,831/74,360 alleles

Filtering AF 19.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 19.6%

Overall 1.17% 18,799/1,612,198 alleles · common exomes 10,126/1,461,824 · genomes 8,673/150,374 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	19.9%	5
Admixed American	1.58%	63
Remaining individualsnot grpmax-eligible	1.58%	63
Middle Eastern	1.55%	64
Ashkenazi Jewishnot grpmax-eligible	0.49%	204
European (non-Finnish)	0.146%	684
South Asian	0.067%	1,492
Finnishnot grpmax-eligible	0.0157%	6,368
East Asian	0.00224%	44,732

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: FLG2
Protein: p.Ala1602=
Coding: c.4806C>T
MANE Select: NM_001014342
dbSNP: rs73007787
Type: single nucleotide variant
Location: chr1:152352980 (GRCh38)

Full FLG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/flg2-p-ala1602 (accessed [today's date]).

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