Is DUSP11 p.Ser72Tyr (c.215C>A) pathogenic?

DUSP11 p.Ser72Tyr (c.215C>A) is classified Uncertain significance in DUSP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-17). AlphaMissense: ambiguous (0.3657); Very rare (popmax 0.00267%, afr).

How common is DUSP11 p.Ser72Tyr (c.215C>A) in the general population?

DUSP11 p.Ser72Tyr (c.215C>A) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about DUSP11 p.Ser72Tyr (c.215C>A)?

AlphaMissense predicts ambiguous (score 0.3657) — an in-silico prediction, not a clinical call.

DUSP11 p.Ser72Tyr

c.215C>A · VCV3505815

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3657 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Computational evidence

Protein change
AlphaMissense	0.3657	ambiguous
REVEL	0.235	benign-leaning
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.2	GERP 1.6, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 17 kb · p 0.86 · regional, not allelic
Overall
CADD	28.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S119Y vs ClinVar S72Y) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,842 alleles

Filtering AF 0.00173% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.00205% 33/1,612,132 alleles · very rare exomes 31/1,459,958 · genomes 2/152,174 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00321%	31,200
African / African-Americangrpmax	0.00267%	37,421
European (non-Finnish)	0.00246%	40,658

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DUSP11
Protein: p.Ser72Tyr
Coding: c.215C>A
MANE Select: NM_003584
Type: single nucleotide variant
Location: chr2:73775007 (GRCh38)
Gene constraint: LOEUF 1.286 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.34 · 3 PDB

Full DUSP11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DUSP11 c.178-7G>C Benign ★★ same type
DUSP11 c.794+5C>G Benign ★★ same type
DUSP11 c.-118G>A Benign ★★ same type
DUSP11 c.-104G>T Uncertain significance ★ ⚠ same type
DUSP11 c.-108G>T Uncertain significance ★ ⚠ same type
DUSP11 c.-116G>A Uncertain significance ★ ⚠ same type
DUSP11 c.-117C>G Uncertain significance ★ ⚠ same type
DUSP11 c.-117C>T 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/dusp11-p-ser72tyr (accessed [today's date]).

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