Is PRDM13 p.Phe31= (c.93C>T) pathogenic?

PRDM13 p.Phe31= (c.93C>T) is classified Likely benign in PRDM13 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-26). Very rare (popmax 8.47e-05%, nfe).

How common is PRDM13 p.Phe31= (c.93C>T) in the general population?

PRDM13 p.Phe31= (c.93C>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

PRDM13 p.Phe31=

c.93C>T · rs757941315 · VCV1099123

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 0.42, phastCons 1
Overall
CADD	13.52	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,028 alleles

Overall 6.2e-05% 1/1,613,992 alleles · very rare exomes 1/1,461,602 · genomes 0/152,390 · 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.Phe31=
Coding: c.93C>T
MANE Select: NM_021620
dbSNP: rs757941315
Type: single nucleotide variant
Location: chr6:99607127 (GRCh38)
Gene constraint: LOEUF 0.694 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 53.52
Residue 31: the set domain

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-phe31 (accessed [today's date]).

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