Is BOLL p.Met122Val (c.364A>G) pathogenic?

BOLL p.Met122Val (c.364A>G) is classified Uncertain significance in BOLL (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-19). AlphaMissense: likely benign (0.0961); Very rare (popmax 0.00501%, nfe).

How common is BOLL p.Met122Val (c.364A>G) in the general population?

BOLL p.Met122Val (c.364A>G) is very rare (popmax 0.00501%, nfe) (gnomAD).

What do computational predictors say about BOLL p.Met122Val (c.364A>G)?

AlphaMissense predicts likely benign (score 0.0961) — an in-silico prediction, not a clinical call.

BOLL p.Met122Val

c.364A>G · VCV4214810

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0961 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00501%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0961	likely benign
REVEL	0.144	moderately benign-leaning
SaProt	LLR -5.04	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 7.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 53 kb · p 0.0053 · regional, not allelic
Overall
CADD	19.77	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 0.00501% European (non-Finnish) · 58/1,158,562 alleles

Filtering AF 0.00393% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00359%

Overall 0.00386% 61/1,582,172 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00501%	19,975
Remaining individualsnot grpmax-eligible	0.00489%	20,452

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: BOLL
Protein: p.Met122Val
Coding: c.364A>G
MANE Select: NM_033030
Type: single nucleotide variant
Location: chr2:197771971 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI 0.31 (gnomAD)
Structure: AlphaFold pLDDT 64.18

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

Similar variants

BOLL p.Ala172Pro Uncertain significance ★ ⚠ same type
BOLL p.Ala172Val Uncertain significance ★ ⚠ same type
BOLL p.Ala185Asp Uncertain significance ★ ⚠ same type
BOLL p.Ala259Asp Uncertain significance ★ ⚠ same type
BOLL p.Ala267Val Uncertain significance ★ ⚠ same type
BOLL p.Arg34Cys Uncertain significance ★ ⚠ same type
BOLL p.Asp85Gly Uncertain significance ★ ⚠ same type
BOLL p.Cys165Gly 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/boll-p-met122val (accessed [today's date]).

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