Is BLTP3B p.Thr1341= (c.4023T>G) pathogenic?

BLTP3B p.Thr1341= (c.4023T>G) is classified Benign in BLTP3B (ClinVar, Single submitter, 2 submitters; last evaluated 2019-12-31). Common (popmax 7.22%, afr) — too common for a highly-penetrant pathogenic allele.

BLTP3B p.Thr1341=

Q: How common is BLTP3B p.Thr1341= (c.4023T>G) in the general population?

BLTP3B p.Thr1341= (c.4023T>G) is common (popmax 7.22%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.4023T>G · rs61739441 · VCV784306

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.22%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.038	moderately benign-leaning
Splicing
SpliceAI	Δ0.27	donor gain · deltas
Constraint at this position
Conservation	phyloP -0.79	GERP -4.6
Overall
CADD	0.953	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.22% African / African-American · 5,414/74,956 alleles

Filtering AF 7.06% ClinGen BA1/BS1 input FAF95, joint · FAF99 7%

Overall 0.394% 6,357/1,613,632 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.22%	14
Admixed American	0.627%	160
Middle Eastern	0.578%	173
Remaining individualsnot grpmax-eligible	0.538%	186
South Asian	0.0231%	4,337
European (non-Finnish)	0.0148%	6,780
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,594

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: BLTP3B
Protein: p.Thr1341=
Coding: c.4023T>G
MANE Select: NM_015054
dbSNP: rs61739441
Type: single nucleotide variant
Location: chr12:100047588 (GRCh38)
Structure: AlphaFold pLDDT 67.53

Full BLTP3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BLTP3B p.Leu491= Benign ★★ same type
BLTP3B p.Ala109Val Uncertain significance ★ ⚠ same type
BLTP3B p.Ala1162Thr Uncertain significance ★ ⚠ same type
BLTP3B p.Ala1272Ser Uncertain significance ★ ⚠ same type
BLTP3B p.Ala231Ser Uncertain significance ★ ⚠ same type
BLTP3B p.Ala231Thr Uncertain significance ★ ⚠ same type
BLTP3B p.Ala257Gly Uncertain significance ★ ⚠ same type
BLTP3B p.Ala66Thr 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/bltp3b-p-thr1341 (accessed [today's date]).

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