Is PRMT1 p.Ala7Val (c.20C>T) pathogenic?

PRMT1 p.Ala7Val (c.20C>T) is classified Uncertain significance in PRMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-02). AlphaMissense: likely benign (0.2205); Ultra-rare (popmax 0.0201%, amr).

How common is PRMT1 p.Ala7Val (c.20C>T) in the general population?

PRMT1 p.Ala7Val (c.20C>T) is ultra-rare (popmax 0.0201%, amr) (gnomAD).

What do computational predictors say about PRMT1 p.Ala7Val (c.20C>T)?

AlphaMissense predicts likely benign (score 0.2205) — an in-silico prediction, not a clinical call.

PRMT1 p.Ala7Val

c.20C>T · VCV4572161

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2205 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0201%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2205	likely benign
REVEL	0.062	moderately benign-leaning
SaProt	LLR -6.70	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 3,251 bp · p 0.73 · regional, not allelic
Overall
CADD	23.0	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

Grpmax group 0.0201% Admixed American · 7/34,846 alleles

Filtering AF 0.00941% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00663%

Overall 0.00135% 19/1,408,994 alleles · ultra-rare exomes 11/1,256,882 · genomes 8/152,112 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0201%	4,978
Remaining individualsnot grpmax-eligible	0.0019%	52,542
South Asian	0.00164%	60,872
African / African-American	0.00149%	67,182
European (non-Finnish)	0.000835%	119,832

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: PRMT1
Protein: p.Ala7Val
Coding: c.20C>T
MANE Select: NM_001536
Type: single nucleotide variant
Location: chr19:49677300 (GRCh38)
Gene constraint: LOEUF 0.218 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.14 · 8 PDB

Full PRMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRMT1 p.Glu45= Benign ★★ same type
PRMT1 p.Ala249Thr Uncertain significance ★ ⚠ same type
PRMT1 p.Ala44Pro Uncertain significance ★ ⚠ same type
PRMT1 p.Arg112His Uncertain significance ★ ⚠ same type
PRMT1 p.Arg195Gln Uncertain significance ★ same type
PRMT1 p.Arg206Gln Uncertain significance ★ ⚠ same type
PRMT1 p.Arg369Gln Uncertain significance ★ ⚠ same type
PRMT1 p.Asn20Lys 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/prmt1-p-ala7val (accessed [today's date]).

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