Is BBIP1 p.Cys51= (c.153T>C) pathogenic?

BBIP1 p.Cys51= (c.153T>C) is classified Likely benign in BBIP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Very rare (popmax 0.00137%, afr).

How common is BBIP1 p.Cys51= (c.153T>C) in the general population?

BBIP1 p.Cys51= (c.153T>C) is very rare (popmax 0.00137%, afr) (gnomAD).

BBIP1 p.Cys51=

c.153T>C · rs1845966177 · VCV1108105

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00137%, afr)

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 9.3	GERP 0.55, phastCons 1
Overall
CADD	12.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00137% African / African-American · 1/73,124 alleles

Overall 7.23e-05% 1/1,383,408 alleles · very rare

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.Cys51=
Coding: c.153T>C
MANE Select: NM_001195305
dbSNP: rs1845966177
Type: single nucleotide variant
Location: chr10:110900486 (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-cys51 (accessed [today's date]).

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