Is BLTP1 p.Arg211His (c.632G>A) pathogenic?

BLTP1 p.Arg211His (c.632G>A) is classified Uncertain significance in BLTP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-22). AlphaMissense: ambiguous (0.49); Very rare (popmax 0.00235%, eas).

How common is BLTP1 p.Arg211His (c.632G>A) in the general population?

BLTP1 p.Arg211His (c.632G>A) is very rare (popmax 0.00235%, eas) (gnomAD).

What do computational predictors say about BLTP1 p.Arg211His (c.632G>A)?

AlphaMissense predicts ambiguous (score 0.49) — an in-silico prediction, not a clinical call.

BLTP1 p.Arg211His

c.632G>A · rs1283898226 · VCV3134226

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.49 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00235%, eas)

Computational evidence

Protein change
AlphaMissense	0.49	ambiguous
REVEL	0.738	pathogenic-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.6	GERP 2.6, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 17 kb · p 0.0013 · regional, not allelic
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00235% East Asian · 1/42,628 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000447% 7/1,565,294 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00235%	42,628
African / African-American	0.0014%	71,292
South Asian	0.00123%	81,424
European (non-Finnish)	0.000344%	291,071

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: BLTP1
Protein: p.Arg211His
Coding: c.632G>A
MANE Select: NM_001384125
dbSNP: rs1283898226
Type: single nucleotide variant
Location: chr4:122187899 (GRCh38)

Full BLTP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
BLTP1 c.1498+4A>G Uncertain significance ★★ same type
BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
BLTP1 p.Arg1317His Uncertain significance ★★ same type
BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
BLTP1 p.Arg2095His Uncertain significance ★★ same type
BLTP1 p.Arg2279Cys Uncertain significance ★★ same type
BLTP1 p.Arg3665Gln 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/bltp1-p-arg211his (accessed [today's date]).

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