Is BASP1 p.Pro100Ser (c.298C>T) pathogenic?

BASP1 p.Pro100Ser (c.298C>T) is classified Uncertain significance in BASP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-16). AlphaMissense: likely benign (0.1078); Ultra-rare (popmax 0.0258%, mid).

How common is BASP1 p.Pro100Ser (c.298C>T) in the general population?

BASP1 p.Pro100Ser (c.298C>T) is ultra-rare (popmax 0.0258%, mid) (gnomAD).

What do computational predictors say about BASP1 p.Pro100Ser (c.298C>T)?

AlphaMissense predicts likely benign (score 0.1078) — an in-silico prediction, not a clinical call.

BASP1 p.Pro100Ser

c.298C>T · rs1386047183 · VCV3133004

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1078 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0258%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1078	likely benign
REVEL	0.095	moderately benign-leaning
SaProt	LLR -5.79	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 0.88	GERP 0.31, phastCons 0.99
Regional constraint	o/e 1.08	unconstrained · MANE · 680 bp · p 0.17 · regional, not allelic
Overall
CADD	17.04	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 0.0258% Middle Eastern · 1/3,882 alleles

Filtering AF 0.000491% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000184%

Overall 0.000465% 6/1,290,618 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0258%	3,882
South Asian	0.00296%	33,799
Remaining individualsnot grpmax-eligible	0.00181%	55,098
European (non-Finnish)	0.000182%	550,852

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: BASP1
Protein: p.Pro100Ser
Coding: c.298C>T
MANE Select: NM_006317
dbSNP: rs1386047183
Type: single nucleotide variant
Location: chr5:17275514 (GRCh38)
Gene constraint: LOEUF 1.32 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 52.18
Residue 100: the 'disordered' region

Full BASP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BASP1 p.Asn13= Benign ★★ same type
BASP1 p.Ala119Val Uncertain significance ★ ⚠ same type
BASP1 p.Ala123Gly Uncertain significance ★ ⚠ same type
BASP1 p.Ala126Val Uncertain significance ★ ⚠ same type
BASP1 p.Ala127Thr Uncertain significance ★ ⚠ same type
BASP1 p.Ala127Val Uncertain significance ★ ⚠ same type
BASP1 p.Ala133Thr Uncertain significance ★ ⚠ same type
BASP1 p.Ala134Thr 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/basp1-p-pro100ser (accessed [today's date]).

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