Is ASB9 p.Ser201Phe (c.602C>T) pathogenic?

ASB9 p.Ser201Phe (c.602C>T) is classified Uncertain significance in ASB9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-05). AlphaMissense: ambiguous (0.5538); Absent from gnomAD v4.1.

How common is ASB9 p.Ser201Phe (c.602C>T) in the general population?

ASB9 p.Ser201Phe (c.602C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ASB9 p.Ser201Phe (c.602C>T)?

AlphaMissense predicts ambiguous (score 0.5538) — an in-silico prediction, not a clinical call.

ASB9 p.Ser201Phe

c.602C>T · rs2519221990 · VCV2299728

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5538 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5538	ambiguous
REVEL	0.491	indeterminate
SaProt	LLR -11.94	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 0.91, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 25 kb · p 0.38 · regional, not allelic
Overall
CADD	21.2	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

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: ASB9
Protein: p.Ser201Phe
Coding: c.602C>T
MANE Select: NM_001031739
dbSNP: rs2519221990
Type: single nucleotide variant
Location: chrX:15248902 (GRCh38)
Structure: AlphaFold pLDDT 91.89 · 4 PDB

Full ASB9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ASB9 p.Ala14Val Uncertain significance ★ ⚠ same type
ASB9 p.Ala181Val Uncertain significance ★ ⚠ same type
ASB9 p.Ala215Gly Uncertain significance ★ same type
ASB9 p.Arg234Cys Uncertain significance ★ ⚠ same type
ASB9 p.Arg267Gln Uncertain significance ★ ⚠ same type
ASB9 p.Gln178Arg Uncertain significance ★ ⚠ same type
ASB9 p.Gln179His Uncertain significance ★ ⚠ same type
ASB9 p.Gln247Lys 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/asb9-p-ser201phe (accessed [today's date]).

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