Is DRP2 p.Pro659Leu (c.1976C>T) pathogenic?

DRP2 p.Pro659Leu (c.1976C>T) is classified Uncertain significance in DRP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-24). AlphaMissense: likely benign (0.2053); Very rare (popmax 0.000676%, nfe).

How common is DRP2 p.Pro659Leu (c.1976C>T) in the general population?

DRP2 p.Pro659Leu (c.1976C>T) is very rare (popmax 0.000676%, nfe) (gnomAD).

What do computational predictors say about DRP2 p.Pro659Leu (c.1976C>T)?

AlphaMissense predicts likely benign (score 0.2053) — an in-silico prediction, not a clinical call.

DRP2 p.Pro659Leu

c.1976C>T · VCV3676896

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2053 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000676%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2053	likely benign
REVEL	0.774	moderately pathogenic-leaning
SaProt	LLR -12.12	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP 0.94, phastCons 1
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000676% European (non-Finnish) · 6/887,116 alleles

Filtering AF 0.000243% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00016%

Overall 0.000552% 6/1,087,672 alleles · very rare

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: DRP2
Protein: p.Pro659Leu
Coding: c.1976C>T
MANE Select: NM_001197293 · reported on NM_001939
Type: single nucleotide variant
Location: chrX:101252715 (GRCh38)
Structure: AlphaFold pLDDT 90.49 · 15 PDB

Full DRP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DRP2 p.Pro659Thr Uncertain significance ★ ⚠ same residue
DRP2 p.Glu432Ter Pathogenic ★★ same type
DPYSL2 p.Asn492Ser Uncertain significance ★★ ⚠ same type
DPYSL2 p.Asp520Asn Uncertain significance ★★ ⚠ same type
DRP2 p.Ala205Val Uncertain significance ★★ ⚠ same type
DRP2 p.Ala643Thr Uncertain significance ★★ ⚠ same type
DRP2 p.Arg199His Uncertain significance ★★ ⚠ same type
DRP2 p.Arg224Cys 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/drp2-p-pro659leu (accessed [today's date]).

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