Is BLTP1 p.Leu4881= (c.14641T>C) pathogenic?

BLTP1 p.Leu4881= (c.14641T>C) is classified Likely benign in BLTP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-16). Ultra-rare (popmax 0.0132%, sas).

How common is BLTP1 p.Leu4881= (c.14641T>C) in the general population?

BLTP1 p.Leu4881= (c.14641T>C) is ultra-rare (popmax 0.0132%, sas) (gnomAD).

BLTP1 p.Leu4881=

c.14641T>C · rs778239176 · VCV3234183

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0132%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.23 · evaluated, not missing
Constraint at this position
Conservation	phyloP -3	GERP -5.1
Overall
CADD	1.903	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0132% South Asian · 12/90,998 alleles

Filtering AF 0.00851% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00796%

Overall 0.0098% 158/1,612,910 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0297%	3,367
South Asiangrpmax	0.0132%	7,583
European (non-Finnish)	0.01%	9,994
Remaining individualsnot grpmax-eligible	0.00801%	12,487
East Asian	0.0067%	14,923
Admixed American	0.00167%	59,982

Finnish 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: BLTP1
Protein: p.Leu4881=
Coding: c.14641T>C
MANE Select: NM_001384125
dbSNP: rs778239176
Type: single nucleotide variant
Location: chr4:122355867 (GRCh38)
Residue 4881: a UniProt-annotated variant site (in alkkucs)

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-leu4881 (accessed [today's date]).

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