Is FLRT1 p.Thr381Arg (c.1142C>G) pathogenic?

FLRT1 p.Thr381Arg (c.1142C>G) is classified Uncertain significance in FLRT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-17). Absent from gnomAD v4.1.

How common is FLRT1 p.Thr381Arg (c.1142C>G) in the general population?

FLRT1 p.Thr381Arg (c.1142C>G) is absent from gnomAD v4.1 (gnomAD).

FLRT1 p.Thr381Arg

c.1142C>G · rs773930935 · VCV3095687

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.059	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.61	GERP -0.7
Regional constraint	o/e 0.78	unconstrained · MANE · 2,021 bp · p 5.7e-12 · regional, not allelic
Overall
CADD	11.8	PHRED · no single calibrated threshold — expert panels disagree

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: FLRT1
Protein: p.Thr381Arg
Coding: c.1142C>G
MANE Select: NM_013280
dbSNP: rs773930935
Type: single nucleotide variant
Location: chr11:64117409 (GRCh38)
Gene constraint: LOEUF 0.682 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 73.46

Full FLRT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FLRT1 p.Thr381Met Uncertain significance ★ same residue
FLRT1 p.Ala148Gly Uncertain significance ★★ same type
FLRT1 p.Ala461Thr Uncertain significance ★★ same type
FLRT1 p.Arg149Cys Uncertain significance ★★ same type
FLRT1 p.Arg326Lys Uncertain significance ★★ same type
FLRT1 p.Arg452His Uncertain significance ★★ same type
FLRT1 p.Arg465Gln Uncertain significance ★★ same type
FLRT1 p.Arg586Gln 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/flrt1-p-thr381arg (accessed [today's date]).

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