Is DIS3L2 p.Ser522Arg (c.1566C>G) pathogenic?

DIS3L2 p.Ser522Arg (c.1566C>G) is classified Uncertain significance in DIS3L2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-09). AlphaMissense: likely benign (0.1619); Very rare (popmax 0.00267%, afr); Associated with Perlman syndrome.

What condition is associated with DIS3L2 p.Ser522Arg (c.1566C>G)?

DIS3L2 p.Ser522Arg (c.1566C>G) is associated with Perlman syndrome (ClinVar).

How common is DIS3L2 p.Ser522Arg (c.1566C>G) in the general population?

DIS3L2 p.Ser522Arg (c.1566C>G) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about DIS3L2 p.Ser522Arg (c.1566C>G)?

AlphaMissense predicts likely benign (score 0.1619) — an in-silico prediction, not a clinical call.

DIS3L2 p.Ser522Arg

c.1566C>G · rs374299868 · VCV661999

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1619 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Perlman syndrome

Computational evidence

Protein change
AlphaMissense	0.1619	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -6.72	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 -12	GERP -1.6
Regional constraint	o/e 0.92	unconstrained · MANE · 319 kb · p 0.024 · regional, not allelic
Overall
CADD	7.396	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

Grpmax group 0.00267% African / African-American · 2/75,046 alleles

Filtering AF 0.000442% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.000205% 3/1,461,890 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,523
Remaining individualsnot grpmax-eligible	0.0016%	62,508

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: DIS3L2
Protein: p.Ser522Arg
Coding: c.1566C>G
MANE Select: NM_152383
dbSNP: rs374299868
Type: single nucleotide variant
Location: chr2:232263347 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 83.26 · 4 PDB

Full DIS3L2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Perlman syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DIS3L2 p.Ser522Gly Uncertain significance ★ ⚠ same residue
DIS3L2 p.Ser522Ile Uncertain significance ★ ⚠ same residue
DIS3L2 p.Ser522= Likely benign ★ same residue
DIS3L2 p.Ser522fs Likely pathogenic ★ same residue
DIS3L2 c.1740-1G>C Likely pathogenic ★★ same condition
DIS3L2 p.Arg245Ter Pathogenic/Likely pathogenic ★★ same condition
DIS3L2 p.Arg388Ter Pathogenic/Likely pathogenic ★★ same condition
DIS3L2 p.Arg43Ter Pathogenic/Likely pathogenic ★★ 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/dis3l2-p-ser522arg (accessed [today's date]).

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