Is DRAXIN p.Pro33Ser (c.97C>T) pathogenic?

DRAXIN p.Pro33Ser (c.97C>T) is classified Likely benign in DRAXIN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-02). AlphaMissense: likely benign (0.0705); Absent from gnomAD v4.1.

How common is DRAXIN p.Pro33Ser (c.97C>T) in the general population?

DRAXIN p.Pro33Ser (c.97C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DRAXIN p.Pro33Ser (c.97C>T)?

AlphaMissense predicts likely benign (score 0.0705) — an in-silico prediction, not a clinical call.

DRAXIN p.Pro33Ser

c.97C>T · VCV4014793

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0705 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0705	likely benign
REVEL	0.022	moderately benign-leaning
SaProt	LLR -6.71	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 -0.2	GERP -3.9
Regional constraint	o/e 0.81	unconstrained · MANE · 13 kb · p 2.9e-05 · regional, not allelic
Overall
CADD	2.216	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: DRAXIN
Protein: p.Pro33Ser
Coding: c.97C>T
MANE Select: NM_198545
Type: single nucleotide variant
Location: chr1:11706355 (GRCh38)
Gene constraint: LOEUF 1.082 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.78 · 1 PDB

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

Similar variants

DRAXIN p.Gly222Arg Benign ★★ same type
DRAXIN p.Ala9Ser Uncertain significance ★ ⚠ same type
DRAXIN p.Arg125Gln Uncertain significance ★ ⚠ same type
DRAXIN p.Arg135Ser Uncertain significance ★ ⚠ same type
DRAXIN p.Arg152Gln Uncertain significance ★ ⚠ same type
DRAXIN p.Arg256His Uncertain significance ★ ⚠ same type
DRAXIN p.Arg329Lys Uncertain significance ★ ⚠ same type
DRAXIN p.Arg58Cys 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/draxin-p-pro33ser (accessed [today's date]).

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