Is BCCIP p.His207Pro (c.620A>C) pathogenic?

BCCIP p.His207Pro (c.620A>C) is classified Uncertain significance in BCCIP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-03). AlphaMissense: likely benign (0.1642); Very rare (popmax 0.00133%, afr).

How common is BCCIP p.His207Pro (c.620A>C) in the general population?

BCCIP p.His207Pro (c.620A>C) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about BCCIP p.His207Pro (c.620A>C)?

AlphaMissense predicts likely benign (score 0.1642) — an in-silico prediction, not a clinical call.

BCCIP p.His207Pro

c.620A>C · rs749157198 · VCV2268838

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1642 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1642	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	LLR -9.96	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP 1.7, phastCons 0.048
Regional constraint	o/e 1.00	unconstrained · MANE · 13 kb · p 0.93 · regional, not allelic
Overall
CADD	20.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,022 alleles

Overall 6.2e-05% 1/1,614,172 alleles · very rare exomes 1/1,461,854 · genomes 0/152,318 · joint denominator

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: BCCIP
Protein: p.His207Pro
Coding: c.620A>C
MANE Select: NM_078468
dbSNP: rs749157198
Type: single nucleotide variant
Location: chr10:125833792 (GRCh38)
Gene constraint: LOEUF 1.053 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 5 PDB
Residue 207: an α-helix; the 'interaction with cdkn1a' region

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

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DHX32 p.Ala619Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Arg572Cys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn448Lys Uncertain significance ★★ ⚠ same type
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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/bccip-p-his207pro (accessed [today's date]).

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