Is BOD1 p.Pro172Ala (c.514C>G) pathogenic?

BOD1 p.Pro172Ala (c.514C>G) is classified Uncertain significance in BOD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-10). AlphaMissense: likely benign (0.0614); Absent from gnomAD v4.1; Associated with BOD1-related Intellectual Disability.

What condition is associated with BOD1 p.Pro172Ala (c.514C>G)?

BOD1 p.Pro172Ala (c.514C>G) is associated with BOD1-related Intellectual Disability (ClinVar).

How common is BOD1 p.Pro172Ala (c.514C>G) in the general population?

BOD1 p.Pro172Ala (c.514C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BOD1 p.Pro172Ala (c.514C>G)?

AlphaMissense predicts likely benign (score 0.0614) — an in-silico prediction, not a clinical call.

BOD1 p.Pro172Ala

c.514C>G · rs1755284095 · VCV983401

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0614 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

BOD1-related Intellectual Disability

Computational evidence

Protein change
AlphaMissense	0.0614	likely benign
REVEL	0.15	moderately benign-leaning
SaProt	LLR -6.69	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 107 bp · p 0.43 · regional, not allelic
Overall
CADD	24.0	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

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: BOD1
Protein: p.Pro172Ala
Coding: c.514C>G
MANE Select: NM_138369
dbSNP: rs1755284095
Type: single nucleotide variant
Location: chr5:173609283 (GRCh38)
Gene constraint: LOEUF 1.335 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.06
Residue 172: the 'disordered' region

Full BOD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BOD1-related Intellectual Disability

Similar variants

BOD1 c.*1+6G>A Likely benign same condition
BOD1 p.Ala158= Likely benign same condition
BOD1 p.Arg151= Likely benign same condition
BOD1 p.Asp183= Likely benign same condition
BOD1 p.Lys161= Likely benign same condition
BOD1 p.Ser181= Likely benign same condition
BOD1 p.Ile153fs Uncertain significance same condition
BOD1 p.Ter186LysextTer? Likely benign same condition

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/bod1-p-pro172ala (accessed [today's date]).

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