Is DEXI p.His9Pro (c.26A>C) pathogenic?

DEXI p.His9Pro (c.26A>C) is classified Uncertain significance in DEXI (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-27). AlphaMissense: likely benign (0.0852); Absent from gnomAD v4.1.

How common is DEXI p.His9Pro (c.26A>C) in the general population?

DEXI p.His9Pro (c.26A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DEXI p.His9Pro (c.26A>C)?

AlphaMissense predicts likely benign (score 0.0852) — an in-silico prediction, not a clinical call.

DEXI p.His9Pro

c.26A>C · rs2145449399 · VCV2239518

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0852 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0852	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -4.99	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.9	GERP 0.88, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 284 bp · p 0.051 · regional, not allelic
Overall
CADD	22.2	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: DEXI
Protein: p.His9Pro
Coding: c.26A>C
MANE Select: NM_000246 · reported on NM_014015
dbSNP: rs2145449399
Type: single nucleotide variant
Location: chr16:10941980 (GRCh38)

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

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/dexi-p-his9pro (accessed [today's date]).

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