Is BLTP1 p.Pro979Ser (c.2935C>T) pathogenic?

BLTP1 p.Pro979Ser (c.2935C>T) is classified Conflicting classifications of pathogenicity in BLTP1 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-03-10). AlphaMissense: likely benign (0.0881); Rare (popmax 0.516%, afr).

How common is BLTP1 p.Pro979Ser (c.2935C>T) in the general population?

BLTP1 p.Pro979Ser (c.2935C>T) is rare (popmax 0.516%, afr) (gnomAD).

What do computational predictors say about BLTP1 p.Pro979Ser (c.2935C>T)?

AlphaMissense predicts likely benign (score 0.0881) — an in-silico prediction, not a clinical call.

BLTP1 p.Pro979Ser

c.2935C>T · rs201348504 · VCV1309577

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0881 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.516%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.0881	likely benign
REVEL	0.116	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.1, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 45 kb · p 1e-08 · regional, not allelic
Overall
CADD	19.64	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.516% African / African-American · 384/74,424 alleles

Filtering AF 0.473% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.457%

Overall 0.0496% 794/1,600,838 alleles · rare exomes 520/1,448,682 · genomes 274/152,156 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.516%	194
Middle Eastern	0.238%	421
Admixed American	0.115%	872
Remaining individualsnot grpmax-eligible	0.111%	898
European (non-Finnish)	0.0221%	4,528
Ashkenazi Jewishnot grpmax-eligible	0.0034%	29,380

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.Pro979Ser
Coding: c.2935C>T
MANE Select: NM_001384125
dbSNP: rs201348504
Type: single nucleotide variant
Location: chr4:122229133 (GRCh38)
Residue 979: 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-pro979ser (accessed [today's date]).

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