Is PRMT7 p.Gln579Pro (c.1736A>C) pathogenic?

PRMT7 p.Gln579Pro (c.1736A>C) is classified Uncertain significance in PRMT7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-24). AlphaMissense: likely benign (0.0843); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with PRMT7 p.Gln579Pro (c.1736A>C)?

PRMT7 p.Gln579Pro (c.1736A>C) is associated with Inborn genetic diseases (ClinVar).

How common is PRMT7 p.Gln579Pro (c.1736A>C) in the general population?

PRMT7 p.Gln579Pro (c.1736A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRMT7 p.Gln579Pro (c.1736A>C)?

AlphaMissense predicts likely benign (score 0.0843) — an in-silico prediction, not a clinical call.

PRMT7 p.Gln579Pro

c.1736A>C · VCV3783468

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0843 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0843	likely benign
REVEL	0.09	moderately benign-leaning
SaProt	LLR -4.90	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.53 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.15	GERP -5.3
Regional constraint	o/e 0.95	unconstrained · MANE · 41 kb · p 0.12 · regional, not allelic
Overall
CADD	6.312	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PRMT7
Protein: p.Gln579Pro
Coding: c.1736A>C
MANE Select: NM_019023
Type: single nucleotide variant
Location: chr16:68355808 (GRCh38)
Gene constraint: LOEUF 1.01 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.19
Residue 579: the sam-dependent mtase prmt-type 2 domain

Full PRMT7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same condition
PRMT7 p.Ala162Thr Uncertain significance ★★ ⚠ same condition
PRMT7 p.Ala332Thr Uncertain significance ★★ ⚠ same condition
PRMT7 p.Ala519Thr Uncertain significance ★★ ⚠ same condition
PRMT7 p.Ala561Gly Uncertain significance ★★ ⚠ same condition
PRMT7 p.Arg177Gly Uncertain significance ★★ ⚠ same condition
PRMT7 p.Arg266Trp Uncertain significance ★★ ⚠ same condition
PRMT7 p.Arg311Trp 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/prmt7-p-gln579pro (accessed [today's date]).

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