Is PRDM13 p.Pro613= (c.1839C>T) pathogenic?

PRDM13 p.Pro613= (c.1839C>T) is classified Likely benign in PRDM13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-16). Very rare (popmax 6.2e-05%).

How common is PRDM13 p.Pro613= (c.1839C>T) in the general population?

PRDM13 p.Pro613= (c.1839C>T) is very rare (popmax 6.2e-05%) (gnomAD).

PRDM13 p.Pro613=

c.1839C>T · VCV3616369

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

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 0.21	GERP -0.28, phastCons 0.97
Overall
CADD	12.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,613,486 alleles · very rare exomes 1/1,461,104 · genomes 0/152,382 · joint denominator

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: PRDM13
Protein: p.Pro613=
Coding: c.1839C>T
MANE Select: NM_021620
Type: single nucleotide variant
Location: chr6:99614474 (GRCh38)
Gene constraint: LOEUF 0.694 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 53.52

Full PRDM13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRDM13 c.277-10T>G Uncertain significance ★★ same type
PRDM13 p.Ala231Val Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala258Val Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala298Pro Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala414Glu Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala510Thr Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala566Thr Uncertain significance ★★ ⚠ same type
PRDM13 p.Ala5Ser 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/prdm13-p-pro613 (accessed [today's date]).

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