Is BBIP1 p.Gln87= (c.261A>G) pathogenic?

BBIP1 p.Gln87= (c.261A>G) is classified Likely benign in BBIP1 (ClinVar, Single submitter, 2 submitters; last evaluated 2019-08-24). Very rare (popmax 0.00589%, amr).

How common is BBIP1 p.Gln87= (c.261A>G) in the general population?

BBIP1 p.Gln87= (c.261A>G) is very rare (popmax 0.00589%, amr) (gnomAD).

BBIP1 p.Gln87=

c.261A>G · rs1287400396 · VCV1162049

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00589%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.5	GERP -3.5
Overall
CADD	0.989	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00589% Admixed American · 3/50,954 alleles

Filtering AF 0.00156% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000833%

Overall 0.000261% 4/1,534,920 alleles · very rare exomes 1/1,382,690 · genomes 3/152,230 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00589%	16,985
Remaining individualsnot grpmax-eligible	0.00167%	59,900

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: BBIP1
Protein: p.Gln87=
Coding: c.261A>G
MANE Select: NM_001195305
dbSNP: rs1287400396
Type: single nucleotide variant
Location: chr10:110900378 (GRCh38)
Gene constraint: LOEUF 1.693 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 82.24 · 1 PDB

Full BBIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BBIP1 c.37+3A>T Uncertain significance ★★ same type
BBIP1 c.38-6T>C Uncertain significance ★★ same type
BBIP1 p.Arg31Trp Uncertain significance ★★ ⚠ same type
BBIP1 p.Arg78His Uncertain significance ★★ ⚠ same type
BBIP1 p.Arg88Gln Uncertain significance ★★ ⚠ same type
BBIP1 p.Asn15Lys Uncertain significance ★★ ⚠ same type
BBIP1 p.Ile17Lys Uncertain significance ★★ ⚠ same type
BBIP1 p.Lys59Asn 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/bbip1-p-gln87 (accessed [today's date]).

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