Is BASP1 p.Gly175Ser (c.523G>A) pathogenic?

BASP1 p.Gly175Ser (c.523G>A) is classified Likely benign in BASP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-15). AlphaMissense: likely benign (0.0575); Very rare (popmax 0.00447%, eas).

How common is BASP1 p.Gly175Ser (c.523G>A) in the general population?

BASP1 p.Gly175Ser (c.523G>A) is very rare (popmax 0.00447%, eas) (gnomAD).

What do computational predictors say about BASP1 p.Gly175Ser (c.523G>A)?

AlphaMissense predicts likely benign (score 0.0575) — an in-silico prediction, not a clinical call.

BASP1 p.Gly175Ser

c.523G>A · VCV3479776

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0575 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00447%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0575	likely benign
REVEL	0.035	moderately benign-leaning
SaProt	LLR -4.38	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 3.2	GERP -2.4, phastCons 0.99
Regional constraint	o/e 1.08	unconstrained · MANE · 680 bp · p 0.17 · regional, not allelic
Overall
CADD	15.81	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 0.00447% East Asian · 2/44,744 alleles

Filtering AF 0.000741% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000206% 3/1,459,544 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00447%	22,372
Remaining individualsnot grpmax-eligible	0.0016%	62,350

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.Gly175Ser
Coding: c.523G>A
MANE Select: NM_006317
Type: single nucleotide variant
Location: chr5:17275739 (GRCh38)
Gene constraint: LOEUF 1.32 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 52.18
Residue 175: 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-gly175ser (accessed [today's date]).

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