Is BOD1L1 p.Arg1069Thr (c.3206G>C) pathogenic?

BOD1L1 p.Arg1069Thr (c.3206G>C) is classified Uncertain significance in BOD1L1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-03). AlphaMissense: likely benign (0.3204); Very rare (popmax 0.000254%, nfe).

How common is BOD1L1 p.Arg1069Thr (c.3206G>C) in the general population?

BOD1L1 p.Arg1069Thr (c.3206G>C) is very rare (popmax 0.000254%, nfe) (gnomAD).

What do computational predictors say about BOD1L1 p.Arg1069Thr (c.3206G>C)?

AlphaMissense predicts likely benign (score 0.3204) — an in-silico prediction, not a clinical call.

BOD1L1 p.Arg1069Thr

c.3206G>C · VCV3481528

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3204 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.3204	likely benign
REVEL	0.072	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.13	GERP -3.3
Regional constraint	o/e 0.99	unconstrained · MANE · 45 kb · p 0.56 · regional, not allelic
Overall
CADD	11.12	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 and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,179,878 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000205% 3/1,461,660 alleles · very rare

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: BOD1L1
Protein: p.Arg1069Thr
Coding: c.3206G>C
MANE Select: NM_148894
Type: single nucleotide variant
Location: chr4:13603694 (GRCh38)
Gene constraint: LOEUF 0.412 · pLI 1.00 (gnomAD)
Residue 1069: the 'disordered' region

Full BOD1L1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BOD1L1 p.Ser2559Phe Uncertain significance ★★ ⚠ same type
BOD1L1 p.Ala1212Thr Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1356Val Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1358Val Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1372Pro Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1410Thr Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1452Asp Uncertain significance ★ ⚠ same type
BOD1L1 p.Ala1506Val 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/bod1l1-p-arg1069thr (accessed [today's date]).

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