Is BEST3 p.Arg141Ser (c.421C>A) pathogenic?

BEST3 p.Arg141Ser (c.421C>A) is classified Uncertain significance in BEST3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-18). AlphaMissense: likely pathogenic (0.9771); Very rare (popmax 0.00153%, nfe).

How common is BEST3 p.Arg141Ser (c.421C>A) in the general population?

BEST3 p.Arg141Ser (c.421C>A) is very rare (popmax 0.00153%, nfe) (gnomAD).

What do computational predictors say about BEST3 p.Arg141Ser (c.421C>A)?

AlphaMissense predicts likely pathogenic (score 0.9771) — an in-silico prediction, not a clinical call.

BEST3 p.Arg141Ser

c.421C>A · VCV3991320

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9771 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00153%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9771	likely pathogenic
REVEL	0.916	moderately pathogenic-leaning
SaProt	LLR -10.53	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.9, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 43 kb · p 0.069 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.00153% European (non-Finnish) · 18/1,180,036 alleles

Filtering AF 0.000953% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000787%

Overall 0.00118% 19/1,614,054 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)grpmax	0.00153%	65,557

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BEST3
Protein: p.Arg141Ser
Coding: c.421C>A
MANE Select: NM_032735
Type: single nucleotide variant
Location: chr12:69693734 (GRCh38)
Gene constraint: LOEUF 1.275 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.66

Full BEST3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BEST3 p.Pro383Leu Benign ★★ same type
BEST3 p.Val49= Benign ★★ same type
BEST3 p.Ala351Gly Uncertain significance ★ ⚠ same type
BEST3 p.Arg196Gln Uncertain significance ★ ⚠ same type
BEST3 p.Arg196Trp Uncertain significance ★ ⚠ same type
BEST3 p.Arg202Ile Uncertain significance ★ ⚠ same type
BEST3 p.Arg216Gly Uncertain significance ★ ⚠ same type
BEST3 p.Arg218Cys 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/best3-p-arg141ser (accessed [today's date]).

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