Is AHSP p.Asp87Val (c.260A>T) pathogenic?

AHSP p.Asp87Val (c.260A>T) is classified Uncertain significance in AHSP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-21). AlphaMissense: likely benign (0.0946); Absent from gnomAD v4.1.

How common is AHSP p.Asp87Val (c.260A>T) in the general population?

AHSP p.Asp87Val (c.260A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AHSP p.Asp87Val (c.260A>T)?

AlphaMissense predicts likely benign (score 0.0946) — an in-silico prediction, not a clinical call.

AHSP p.Asp87Val

c.260A>T · rs2544913081 · VCV2527659

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0946 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0946	likely benign
REVEL	0.216	benign-leaning
SaProt	LLR -8.20	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 -0.12	GERP -3.1
Regional constraint	o/e 1.12	unconstrained · MANE · 548 bp · p 0.19 · regional, not allelic
Overall
CADD	5.688	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: AHSP
Protein: p.Asp87Val
Coding: c.260A>T
MANE Select: NM_016633
dbSNP: rs2544913081
Type: single nucleotide variant
Location: chr16:31528642 (GRCh38)
Gene constraint: LOEUF 1.947 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.37 · 8 PDB
Residue 87: a turn

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

Similar variants

AHSP p.Pro100Thr Benign/Likely benign ★★ same type
AHSP p.Ala13Pro Uncertain significance ★ ⚠ same type
AHSP p.Ala6Ser Uncertain significance ★ ⚠ same type
AHSP p.Asn46Asp Uncertain significance ★ ⚠ same type
AHSP p.Asn75Ile Uncertain significance ★ ⚠ same type
AHSP p.Asp43Gly Uncertain significance ★ ⚠ same type
AHSP p.Asp64Gly Uncertain significance ★ ⚠ same type
AHSP p.Gln24His 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/ahsp-p-asp87val (accessed [today's date]).

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