Is PRDM6 p.Pro71= (c.213G>T) pathogenic?

PRDM6 p.Pro71= (c.213G>T) is classified Likely benign in PRDM6 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-23). Ultra-rare (popmax 0.0162%, afr).

How common is PRDM6 p.Pro71= (c.213G>T) in the general population?

PRDM6 p.Pro71= (c.213G>T) is ultra-rare (popmax 0.0162%, afr) (gnomAD).

PRDM6 p.Pro71=

c.213G>T · VCV4971760

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0162%, afr)

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 0.77	GERP 1, phastCons 0.99
Overall
CADD	14.07	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0162% African / African-American · 11/67,990 alleles

Filtering AF 0.00905% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00701%

Overall 0.00387% 57/1,473,066 alleles · ultra-rare exomes 45/1,321,404 · genomes 12/151,662 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0162%	6,181
European (non-Finnish)	0.00404%	24,740
Remaining individualsnot grpmax-eligible	0.00177%	56,384

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: PRDM6
Protein: p.Pro71=
Coding: c.213G>T
MANE Select: NM_001136239
Type: single nucleotide variant
Location: chr5:123090227 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI 0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 57.72
Residue 71: the 'disordered' region

Full PRDM6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRDM6 p.Leu26Phe Uncertain significance ★★ ⚠ same type
PRDM6 p.Lys149Met Uncertain significance ★★ ⚠ same type
PRDM6 p.Ser78Cys Uncertain significance ★★ ⚠ same type
PRDM6 p.Cys503= Likely benign ★★ same type
PRDM6 p.Gly153= Likely benign ★★ same type
PRDM6 p.Pro56= Likely benign ★★ same type
PRDM6 p.Ala101Pro Uncertain significance ★ ⚠ same type
PRDM6 p.Ala102Pro 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/prdm6-p-pro71 (accessed [today's date]).

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