Is BLCAP p.Pro74Ser (c.220C>T) pathogenic?

BLCAP p.Pro74Ser (c.220C>T) is classified Uncertain significance in BLCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-06). AlphaMissense: likely benign (0.0588); Absent from gnomAD v4.1.

How common is BLCAP p.Pro74Ser (c.220C>T) in the general population?

BLCAP p.Pro74Ser (c.220C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BLCAP p.Pro74Ser (c.220C>T)?

AlphaMissense predicts likely benign (score 0.0588) — an in-silico prediction, not a clinical call.

BLCAP p.Pro74Ser

c.220C>T · rs2515226460 · VCV2557669

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0588 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0588	likely benign
REVEL	0.021	moderately benign-leaning
SaProt	LLR -5.70	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 9.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.61	unconstrained · MANE · 260 bp · p 6e-05 · regional, not allelic
Overall
CADD	21.6	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

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: BLCAP
Protein: p.Pro74Ser
Coding: c.220C>T
MANE Select: NM_006698
dbSNP: rs2515226460
Type: single nucleotide variant
Location: chr20:37518955 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI 0.72 (gnomAD)
Structure: AlphaFold pLDDT 63.24

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

Similar variants

BLCAP p.Pro74Leu Uncertain significance ★ ⚠ same residue
BLCAP p.Glu39Gln Uncertain significance ★ ⚠ same type
BLCAP p.Gly83Ser Uncertain significance ★ ⚠ same type
BLCAP p.Tyr59Cys Uncertain significance ★ ⚠ same type
BLCAP p.Val85Met Uncertain significance ★ ⚠ same type
NNAT p.Ala6Val Uncertain significance ★ ⚠ same type
NNAT p.Arg76Trp Uncertain significance ★ ⚠ same type
NNAT p.Gln45Leu 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/blcap-p-pro74ser (accessed [today's date]).

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