Is A4GNT p.Ser98Pro (c.292T>C) pathogenic?

A4GNT p.Ser98Pro (c.292T>C) is classified Likely benign in A4GNT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-11). AlphaMissense: likely benign (0.0592); Absent from gnomAD v4.1.

How common is A4GNT p.Ser98Pro (c.292T>C) in the general population?

A4GNT p.Ser98Pro (c.292T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about A4GNT p.Ser98Pro (c.292T>C)?

AlphaMissense predicts likely benign (score 0.0592) — an in-silico prediction, not a clinical call.

A4GNT p.Ser98Pro

c.292T>C · rs2472928301 · VCV2289372

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0592 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0592	likely benign
REVEL	0.047	moderately benign-leaning
SaProt	LLR -8.63	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 1.2	GERP -3, phastCons 0.85
Regional constraint	o/e 0.90	unconstrained · MANE · 6,989 bp · p 0.05 · regional, not allelic
Overall
CADD	9.736	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: A4GNT
Protein: p.Ser98Pro
Coding: c.292T>C
MANE Select: NM_016161
dbSNP: rs2472928301
Type: single nucleotide variant
Location: chr3:138130965 (GRCh38)
Gene constraint: LOEUF 1.375 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 89.43

Full A4GNT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

A4GNT p.Arg266Ter Likely benign ★★ same type
A4GNT p.Ala141Pro Uncertain significance ★ ⚠ same type
A4GNT p.Ala141Thr Uncertain significance ★ ⚠ same type
A4GNT p.Ala186Asp Uncertain significance ★ ⚠ same type
A4GNT p.Ala186Thr Uncertain significance ★ ⚠ same type
A4GNT p.Arg154Cys Uncertain significance ★ ⚠ same type
A4GNT p.Arg154Ser Uncertain significance ★ ⚠ same type
A4GNT p.Arg188Trp 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/a4gnt-p-ser98pro (accessed [today's date]).

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