Is FLRT3 p.Ser30= (c.90C>A) pathogenic?

FLRT3 p.Ser30= (c.90C>A) is classified Likely benign in FLRT3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-04). Ultra-rare (popmax 0.0197%, nfe).

How common is FLRT3 p.Ser30= (c.90C>A) in the general population?

FLRT3 p.Ser30= (c.90C>A) is ultra-rare (popmax 0.0197%, nfe) (gnomAD).

FLRT3 p.Ser30=

c.90C>A · rs763623092 · VCV795201

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0197%, nfe)

⚠ 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; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.2	GERP 1.3, phastCons 1
Overall
CADD	7.57	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0197% European (non-Finnish) · 232/1,179,694 alleles

Filtering AF 0.0176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0168%

Overall 0.0151% 244/1,613,520 alleles · ultra-rare exomes 228/1,461,422 · genomes 16/152,098 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0197%	5,085
Remaining individualsnot grpmax-eligible	0.0112%	8,923
African / African-American	0.00401%	24,961
Finnishnot grpmax-eligible	0.00312%	32,016

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: FLRT3
Protein: p.Ser30=
Coding: c.90C>A
MANE Select: NM_198391
dbSNP: rs763623092
Type: single nucleotide variant
Location: chr20:14327417 (GRCh38)

Full FLRT3 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/flrt3-p-ser30 (accessed [today's date]).

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