Is BPI p.Glu212Lys (c.634G>A) pathogenic?

BPI p.Glu212Lys (c.634G>A) is classified Benign in BPI (ClinVar, Multiple submitters, 2 submitters; last evaluated 2016-03-28). AlphaMissense: likely benign (0.0738); Common (popmax 50.5%, afr) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about BPI p.Glu212Lys (c.634G>A)?

AlphaMissense predicts likely benign (score 0.0738) — an in-silico prediction, not a clinical call.

BPI p.Glu212Lys

Q: How common is BPI p.Glu212Lys (c.634G>A) in the general population?

BPI p.Glu212Lys (c.634G>A) is common (popmax 50.5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.634G>A · rs4358188 · VCV402434

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0738 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 50.5%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0738	likely benign
REVEL	0.201	benign-leaning
SaProt	LLR -4.62	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 -0.28	GERP -5
Regional constraint	o/e 1.07	unconstrained · MANE · 33 kb · p 0.094 · regional, not allelic
Overall
CADD	0.041	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM E216K vs ClinVar E212K) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 50.5% African / African-American · 37,786/74,888 alleles

Filtering AF 50.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 49.9%

Overall 47.6% 767,228/1,612,388 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	59.7%	2
Finnishnot grpmax-eligible	56.1%	2
African / African-Americangrpmax	50.5%	2
South Asian	50.4%	2
European (non-Finnish)	48.4%	2
Remaining individualsnot grpmax-eligible	46.1%	2
Middle Eastern	44%	2
Admixed American	40.5%	2
Ashkenazi Jewishnot grpmax-eligible	39.9%	3
East Asian	20.9%	5

Amish 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: BPI
Protein: p.Glu212Lys
Coding: c.634G>A
MANE Select: NM_001725
dbSNP: rs4358188
Type: single nucleotide variant
Location: chr20:38318446 (GRCh38)
Gene constraint: LOEUF 1.011 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.70 · 2 PDB
Residue 212: the 'n-terminal barrel' region; an α-helix

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

Similar variants

BPI c.664+7G>T Benign ★★ same type
BPI p.Ala12Val Benign ★★ same type
BPI p.Ala192Val Benign ★★ same type
BPI p.Ala333Thr Likely benign ★★ ⚠ same type
BPI p.Ala8Thr Benign ★★ same type
BPI p.Ala8Val Benign ★★ same type
BPI p.Arg86Cys Benign ★★ ⚠ same type
BPI p.Glu136Gln Benign ★★ 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/bpi-p-glu212lys (accessed [today's date]).

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