Is PRDM16 p.Pro659= (c.1977G>A) pathogenic?

PRDM16 p.Pro659= (c.1977G>A) is classified Likely benign in PRDM16 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-14). Ultra-rare (popmax 0.0168%, mid); Associated with left ventricular noncompaction 8.

What condition is associated with PRDM16 p.Pro659= (c.1977G>A)?

PRDM16 p.Pro659= (c.1977G>A) is associated with left ventricular noncompaction 8 (ClinVar).

How common is PRDM16 p.Pro659= (c.1977G>A) in the general population?

PRDM16 p.Pro659= (c.1977G>A) is ultra-rare (popmax 0.0168%, mid) (gnomAD).

How is Left ventricular noncompaction inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PRDM16 p.Pro659=

c.1977G>A · rs759550479 · VCV227863

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0168%, mid)

Conditions

left ventricular noncompaction 8

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 -4.6	GERP -4.2
Overall
CADD	1.185	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0168% Middle Eastern · 1/5,948 alleles

Filtering AF 0.000909% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000547%

Overall 0.00145% 23/1,584,624 alleles · ultra-rare exomes 22/1,432,450 · genomes 1/152,174 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0168%	5,948
Remaining individualsnot grpmax-eligible	0.00491%	20,359
South Asian	0.00342%	29,212
Finnishnot grpmax-eligible	0.00161%	61,966
African / African-American	0.00135%	74,222
European (non-Finnish)	0.0012%	83,021

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: PRDM16
Protein: p.Pro659=
Coding: c.1977G>A
MANE Select: NM_022114
dbSNP: rs759550479
Type: single nucleotide variant
Location: chr1:3412174 (GRCh38)
Gene constraint: LOEUF 0.304 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 51.73 · 2 PDB

Full PRDM16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

left ventricular noncompaction 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Left ventricular noncompaction (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: All ages

Similar variants

PRDM16 p.Pro659Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
PRDM16 c.388-2A>G Uncertain significance ★★ same condition
PRDM16 p.Ala1035Ser Uncertain significance ★★ ⚠ same condition
PRDM16 p.Ala106Thr Uncertain significance ★★ ⚠ same condition
PRDM16 p.Ala1096Thr Uncertain significance ★★ ⚠ same condition
PRDM16 p.Ala1096Val Uncertain significance ★★ ⚠ same condition
PRDM16 p.Ala1146Thr Uncertain significance ★★ ⚠ same condition
PRDM16 p.Ala175Val Uncertain significance ★★ ⚠ 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/prdm16-p-pro659 (accessed [today's date]).

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