Is DSE p.Met297Ile (c.891G>A) pathogenic?

DSE p.Met297Ile (c.891G>A) is classified Uncertain significance in DSE (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-01). AlphaMissense: ambiguous (0.5424); Ultra-rare (popmax 0.0245%, eas).

How common is DSE p.Met297Ile (c.891G>A) in the general population?

DSE p.Met297Ile (c.891G>A) is ultra-rare (popmax 0.0245%, eas) (gnomAD).

What do computational predictors say about DSE p.Met297Ile (c.891G>A)?

AlphaMissense predicts ambiguous (score 0.5424) — an in-silico prediction, not a clinical call.

DSE p.Met297Ile

c.891G>A · rs768909519 · VCV2442726

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5424 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0245%, eas)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5424	ambiguous
REVEL	0.159	moderately benign-leaning
SaProt	LLR -3.23	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 36 kb · p 6.1e-20 · regional, not allelic
Overall
CADD	22.4	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

Grpmax group 0.0245% East Asian · 11/44,890 alleles

Filtering AF 0.0137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.00103% 15/1,461,834 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0245%	4,081
African / African-American	0.00133%	75,048
European (non-Finnish)	0.000254%	393,342

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DSE
Protein: p.Met297Ile
Coding: c.891G>A
MANE Select: NM_013352
dbSNP: rs768909519
Type: single nucleotide variant
Location: chr6:116431174 (GRCh38)
Gene constraint: LOEUF 0.563 · pLI 0.06 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.59 · 1 PDB
Residue 297: an α-helix

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

Similar variants

TSPYL1 p.Asp297Tyr Uncertain significance ★ ⚠ same residue
DSE c.416+1G>A Likely pathogenic ★★ same type
DSE p.Ala122Thr Uncertain significance ★★ ⚠ same type
DSE p.Ala135Val Uncertain significance ★★ ⚠ same type
DSE p.Ala408Thr Uncertain significance ★★ ⚠ same type
DSE p.Ala54Val Uncertain significance ★★ ⚠ same type
DSE p.Ala584Val Uncertain significance ★★ ⚠ same type
DSE p.Ala688Val 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/dse-p-met297ile (accessed [today's date]).

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