Is DUSP22 p.Val106Ile (c.316G>A) pathogenic?

DUSP22 p.Val106Ile (c.316G>A) is classified Likely benign in DUSP22 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-06-13). AlphaMissense: likely benign (0.1003); Rare (popmax 0.669%, eas); Associated with DUSP22-related disorder.

What condition is associated with DUSP22 p.Val106Ile (c.316G>A)?

DUSP22 p.Val106Ile (c.316G>A) is associated with DUSP22-related disorder (ClinVar).

How common is DUSP22 p.Val106Ile (c.316G>A) in the general population?

DUSP22 p.Val106Ile (c.316G>A) is rare (popmax 0.669%, eas) (gnomAD).

What do computational predictors say about DUSP22 p.Val106Ile (c.316G>A)?

AlphaMissense predicts likely benign (score 0.1003) — an in-silico prediction, not a clinical call.

DUSP22 p.Val106Ile

c.316G>A · rs202152797 · VCV3035033

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1003 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.669%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DUSP22-related disorder

Computational evidence

Protein change
AlphaMissense	0.1003	likely benign
REVEL	0.234	benign-leaning
SaProt	LLR -9.55	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 2.2	GERP -0.16, phastCons 0.99
Regional constraint	o/e 1.23	unconstrained · MANE · 56 kb · p 0.00021 · regional, not allelic
Overall
CADD	16.45	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 0.669% East Asian · 300/44,842 alleles

Filtering AF 0.607% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.582%

Overall 0.0383% 619/1,614,142 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.669%	149
Ashkenazi Jewishnot grpmax-eligible	0.335%	299
African / African-American	0.0786%	1,272
Remaining individualsnot grpmax-eligible	0.0608%	1,645
Admixed American	0.055%	1,819
South Asian	0.00878%	11,386
European (non-Finnish)	0.00695%	14,391

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: DUSP22
Protein: p.Val106Ile
Coding: c.316G>A
MANE Select: NM_001286555
dbSNP: rs202152797
Type: single nucleotide variant
Location: chr6:348155 (GRCh38)
Gene constraint: LOEUF 1.407 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.64 · 8 PDB
Residue 106: the tyrosine-protein phosphatase domain; an α-helix

Full DUSP22 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DUSP22-related disorder

Similar variants

DUSP22 c.189-4C>T Likely benign same condition
DUSP22 c.-5C>T Likely benign same condition
DUSP22 c.*1871C>G Likely benign same condition
DUSP22 c.*1878G>A Benign same condition
DUSP22 c.*2G>A Likely benign same condition
DUSP22 c.*8G>A Likely benign same condition
DUSP22 p.Ala23= Likely benign same condition
DUSP22 p.Ala56= Likely benign same condition

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/dusp22-p-val106ile (accessed [today's date]).

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