Is BCCIP p.Ser5Pro (c.13T>C) pathogenic?

BCCIP p.Ser5Pro (c.13T>C) is classified Likely benign in BCCIP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-11). AlphaMissense: likely benign (0.0555); Very rare (popmax 0.00483%, nfe).

How common is BCCIP p.Ser5Pro (c.13T>C) in the general population?

BCCIP p.Ser5Pro (c.13T>C) is very rare (popmax 0.00483%, nfe) (gnomAD).

What do computational predictors say about BCCIP p.Ser5Pro (c.13T>C)?

AlphaMissense predicts likely benign (score 0.0555) — an in-silico prediction, not a clinical call.

BCCIP p.Ser5Pro

c.13T>C · rs755788724 · VCV2288932

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0555 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00483%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0555	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -6.62	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 -0.078	GERP -3.4, phastCons 0.094
Regional constraint	o/e 1.00	unconstrained · MANE · 13 kb · p 0.93 · regional, not allelic
Overall
CADD	0.895	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

Grpmax group 0.00483% European (non-Finnish) · 57/1,179,854 alleles

Filtering AF 0.00378% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00345%

Overall 0.0039% 63/1,613,524 alleles · very rare exomes 61/1,461,534 · genomes 2/151,990 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00483%	20,699
South Asian	0.00439%	22,766
Admixed American	0.00167%	59,994
Remaining individualsnot grpmax-eligible	0.0016%	62,466

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.Ser5Pro
Coding: c.13T>C
MANE Select: NM_078468
dbSNP: rs755788724
Type: single nucleotide variant
Location: chr10:125823570 (GRCh38)
Gene constraint: LOEUF 1.053 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 5 PDB
Residue 5: the 'disordered' region

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

Similar variants

DHX32 p.Ala496Val Uncertain significance ★★ ⚠ same type
DHX32 p.Ala510Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Ala529Ser Uncertain significance ★★ ⚠ same type
DHX32 p.Ala619Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Arg572Cys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn448Lys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn473His Uncertain significance ★★ ⚠ same type
DHX32 p.Asp585Ala 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/bccip-p-ser5pro (accessed [today's date]).

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