Is BLTP1 p.Pro474= (c.1422G>A) pathogenic?

BLTP1 p.Pro474= (c.1422G>A) is classified Likely benign in BLTP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-02-03). Ultra-rare (popmax 0.0374%, afr); Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Pro474= (c.1422G>A)?

BLTP1 p.Pro474= (c.1422G>A) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Pro474= (c.1422G>A) in the general population?

BLTP1 p.Pro474= (c.1422G>A) is ultra-rare (popmax 0.0374%, afr) (gnomAD).

BLTP1 p.Pro474=

c.1422G>A · rs367630109 · VCV3049027

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0374%, afr)

Conditions

BLTP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.085	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.3	GERP -5.4
Overall
CADD	7.245	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0374% African / African-American · 28/74,828 alleles

Filtering AF 0.0266% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0229%

Overall 0.00397% 64/1,613,228 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0374%	2,672
European (non-Finnish)	0.00288%	34,699
Admixed American	0.00167%	59,824
South Asian	0.0011%	90,940

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.Pro474=
Coding: c.1422G>A
MANE Select: NM_001384125
dbSNP: rs367630109
Type: single nucleotide variant
Location: chr4:122201050 (GRCh38)

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

Disease context

BLTP1-related disorder

Similar variants

BLTP1 p.Pro474Leu Uncertain significance ★ same residue
BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same condition
BLTP1 p.His3063Arg Uncertain significance ★★ same condition
BLTP1 c.10312+2T>C Likely pathogenic ★ same condition
BLTP1 c.11513+1G>C Likely pathogenic ★ same condition
BLTP1 c.5184+1G>T Likely pathogenic ★ same condition
BLTP1 p.Arg3190Ter Likely pathogenic ★ same condition
BLTP1 p.Phe3799Ser Uncertain significance ★ same condition

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-pro474 (accessed [today's date]).

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