Is BLTP1 p.Pro220= (c.660G>T) pathogenic?

BLTP1 p.Pro220= (c.660G>T) is classified Likely benign in BLTP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-03-01). Very rare (popmax 0.00137%, nfe); Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Pro220= (c.660G>T)?

BLTP1 p.Pro220= (c.660G>T) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Pro220= (c.660G>T) in the general population?

BLTP1 p.Pro220= (c.660G>T) is very rare (popmax 0.00137%, nfe) (gnomAD).

BLTP1 p.Pro220=

c.660G>T · rs138600216 · VCV3046186

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00137%, nfe)

Conditions

BLTP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.065	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.52	GERP -3.2, phastCons 0.059
Overall
CADD	2.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00137% European (non-Finnish) · 16/1,169,076 alleles

Filtering AF 0.00081% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000656%

Overall 0.00126% 18/1,431,114 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00167%	60,050
Remaining individualsnot grpmax-eligible	0.00163%	61,400
European (non-Finnish)grpmax	0.00137%	73,067

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.Pro220=
Coding: c.660G>T
MANE Select: NM_001384125
dbSNP: rs138600216
Type: single nucleotide variant
Location: chr4:122187927 (GRCh38)

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

Disease context

BLTP1-related disorder

Similar variants

BLTP1 p.Pro220Leu 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-pro220 (accessed [today's date]).

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