Is PRMT7 p.Arg53Trp (c.157C>T) pathogenic?

PRMT7 p.Arg53Trp (c.157C>T) is classified Uncertain significance in PRMT7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-23). AlphaMissense: likely benign (0.1672); Ultra-rare (popmax 0.0183%, amr); Associated with Inborn genetic diseases.

What condition is associated with PRMT7 p.Arg53Trp (c.157C>T)?

PRMT7 p.Arg53Trp (c.157C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PRMT7 p.Arg53Trp (c.157C>T) in the general population?

PRMT7 p.Arg53Trp (c.157C>T) is ultra-rare (popmax 0.0183%, amr) (gnomAD).

What do computational predictors say about PRMT7 p.Arg53Trp (c.157C>T)?

AlphaMissense predicts likely benign (score 0.1672) — an in-silico prediction, not a clinical call.

PRMT7 p.Arg53Trp

c.157C>T · rs756722562 · VCV2407836

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1672 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0183%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1672	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -10.39	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.2	GERP 1.4, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 41 kb · p 0.12 · regional, not allelic
Overall
CADD	24.7	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 0.0183% Admixed American · 11/60,012 alleles

Filtering AF 0.0102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00785%

Overall 0.00688% 111/1,614,094 alleles · ultra-rare exomes 92/1,461,856 · genomes 19/152,238 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0183%	5,456
European (non-Finnish)	0.00737%	13,563
East Asian	0.00668%	14,966
African / African-American	0.00667%	14,990
Remaining individualsnot grpmax-eligible	0.0064%	15,622
South Asian	0.0011%	91,088

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: PRMT7
Protein: p.Arg53Trp
Coding: c.157C>T
MANE Select: NM_019023
dbSNP: rs756722562
Type: single nucleotide variant
Location: chr16:68324707 (GRCh38)
Gene constraint: LOEUF 1.01 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.19
Residue 53: the sam-dependent mtase prmt-type 1 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-arg53trp (accessed [today's date]).

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