Is ZNF513 p.Pro366= (c.1098C>T) pathogenic?

ZNF513 p.Pro366= (c.1098C>T) is classified Uncertain significance in ZNF513 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). Ultra-rare (popmax 0.0379%, eas); Associated with inherited retinal dystrophy.

What condition is associated with ZNF513 p.Pro366= (c.1098C>T)?

ZNF513 p.Pro366= (c.1098C>T) is associated with inherited retinal dystrophy (ClinVar).

How common is ZNF513 p.Pro366= (c.1098C>T) in the general population?

ZNF513 p.Pro366= (c.1098C>T) is ultra-rare (popmax 0.0379%, eas) (gnomAD).

ZNF513 p.Pro366=

c.1098C>T · rs771856726 · VCV3028782

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0379%, eas)

Conditions

inherited retinal dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.18	GERP -1.1, phastCons 0.86
Overall
CADD	7.659	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0379% East Asian · 17/44,800 alleles

Filtering AF 0.0241% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0198%

Overall 0.00118% 19/1,611,338 alleles · ultra-rare exomes 17/1,458,998 · genomes 2/152,340 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0379%	2,635
European (non-Finnish)	0.00017%	589,084

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: ZNF513
Protein: p.Pro366=
Coding: c.1098C>T
MANE Select: NM_144631
dbSNP: rs771856726
Type: single nucleotide variant
Location: chr2:27378073 (GRCh38)
Gene constraint: LOEUF 0.615 · pLI 0.41 (gnomAD)
Structure: AlphaFold pLDDT 60.20

Full ZNF513 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ZNF513 p.Pro366Ser Uncertain significance ★ ⚠ same residue
ZNF513 p.Arg207Cys Uncertain significance ★★ ⚠ same condition
ZNF513 p.Arg247Gln Uncertain significance ★★ ⚠ same condition
ZNF513 p.Arg263Trp Uncertain significance ★★ ⚠ same condition
ZNF513 p.Arg338His Uncertain significance ★★ ⚠ same condition
ZNF513 p.Arg341Gln Uncertain significance ★★ ⚠ same condition
ZNF513 p.Ala396= Likely benign ★★ same condition
ZNF513 p.Ala260= Conflicting classifications of pathogenicity ★ 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/znf513-p-pro366 (accessed [today's date]).

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