Is BCL7C p.Pro160Ser (c.478C>T) pathogenic?

BCL7C p.Pro160Ser (c.478C>T) is classified Uncertain significance in BCL7C (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-18). AlphaMissense: likely pathogenic (0.9033); Absent from gnomAD v4.1.

How common is BCL7C p.Pro160Ser (c.478C>T) in the general population?

BCL7C p.Pro160Ser (c.478C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BCL7C p.Pro160Ser (c.478C>T)?

AlphaMissense predicts likely pathogenic (score 0.9033) — an in-silico prediction, not a clinical call.

BCL7C p.Pro160Ser

c.478C>T · VCV3991043

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9033 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9033	likely pathogenic
REVEL	0.172	moderately benign-leaning
SaProt	LLR -6.67	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 6,076 bp · p 0.035 · regional, not allelic
Overall
CADD	26.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BCL7C
Protein: p.Pro160Ser
Coding: c.478C>T
MANE Select: NM_004765
Type: single nucleotide variant
Location: chr16:30888910 (GRCh38)
Gene constraint: LOEUF 0.546 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 63.71
Residue 160: the 'disordered' region

Full BCL7C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCL7C p.Arg209His Uncertain significance ★ ⚠ same type
BCL7C p.Arg70His Uncertain significance ★ ⚠ same type
BCL7C p.Arg74Cys Uncertain significance ★ ⚠ same type
BCL7C p.Arg75Gln Uncertain significance ★ ⚠ same type
BCL7C p.Arg82Gln Uncertain significance ★ ⚠ same type
BCL7C p.Asp94Gly Uncertain significance ★ ⚠ same type
BCL7C p.Glu146Gln Uncertain significance ★ ⚠ same type
BCL7C p.Glu179Lys 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/bcl7c-p-pro160ser (accessed [today's date]).

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