Is BLTP2 p.Asp833Ala (c.2498A>C) pathogenic?

BLTP2 p.Asp833Ala (c.2498A>C) is classified Likely benign in BLTP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-30). AlphaMissense: likely benign (0.3019); Rare (popmax 0.216%, afr).

How common is BLTP2 p.Asp833Ala (c.2498A>C) in the general population?

BLTP2 p.Asp833Ala (c.2498A>C) is rare (popmax 0.216%, afr) (gnomAD).

What do computational predictors say about BLTP2 p.Asp833Ala (c.2498A>C)?

AlphaMissense predicts likely benign (score 0.3019) — an in-silico prediction, not a clinical call.

BLTP2 p.Asp833Ala

c.2498A>C · rs77520749 · VCV738500

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3019 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.216%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3019	likely benign
REVEL	0.236	benign-leaning
SaProt	LLR -5.91	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 0.91, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 10 kb · p 0.6 · regional, not allelic
Overall
CADD	25.3	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 0.216% African / African-American · 162/74,832 alleles

Filtering AF 0.189% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.179%

Overall 0.0109% 176/1,613,218 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.216%	462
Remaining individualsnot grpmax-eligible	0.0144%	6,944
Admixed American	0.00834%	11,996

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: BLTP2
Protein: p.Asp833Ala
Coding: c.2498A>C
MANE Select: NM_014680
dbSNP: rs77520749
Type: single nucleotide variant
Location: chr17:28635089 (GRCh38)
Structure: AlphaFold pLDDT 71.37

Full BLTP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BLTP2 p.Ala1395Ser Uncertain significance ★ ⚠ same type
BLTP2 p.Ala1564Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala1826Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala248Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala324Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala393Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala539Thr Uncertain significance ★ ⚠ same type
BLTP2 p.Ala694Gly 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/bltp2-p-asp833ala (accessed [today's date]).

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