Is PRMT6 p.Pro314= (c.942G>A) pathogenic?

PRMT6 p.Pro314= (c.942G>A) is classified Benign in PRMT6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-30). Low-frequency (popmax 1.82%, sas); Associated with PRMT6-related disorder.

What condition is associated with PRMT6 p.Pro314= (c.942G>A)?

PRMT6 p.Pro314= (c.942G>A) is associated with PRMT6-related disorder (ClinVar).

How common is PRMT6 p.Pro314= (c.942G>A) in the general population?

PRMT6 p.Pro314= (c.942G>A) is low-frequency (popmax 1.82%, sas) (gnomAD).

PRMT6 p.Pro314=

c.942G>A · rs2232017 · VCV3041430

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.82%, sas)

Conditions

PRMT6-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.08	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -3.6
Overall
CADD	7.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.82% South Asian · 1,662/91,086 alleles

Filtering AF 1.75% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.72%

Overall 0.957% 15,447/1,614,224 alleles · low-frequency exomes 14,467/1,461,892 · genomes 980/152,332 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	1.82%	55
Amishnot grpmax-eligible	1.76%	57
European (non-Finnish)	1.08%	92
Remaining individualsnot grpmax-eligible	0.808%	124
Admixed American	0.34%	294
Middle Eastern	0.297%	337
Finnishnot grpmax-eligible	0.239%	419
African / African-American	0.133%	751
Ashkenazi Jewishnot grpmax-eligible	0.0946%	1,057
East Asian	0.00446%	22,437

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: PRMT6
Protein: p.Pro314=
Coding: c.942G>A
MANE Select: NM_018137
dbSNP: rs2232017
Type: single nucleotide variant
Location: chr1:107057657 (GRCh38)
Gene constraint: LOEUF 1.052 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.80 · 13 PDB
Residue 314: the sam-dependent mtase prmt-type domain

Full PRMT6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PRMT6-related disorder

Similar variants

PRMT6 p.Pro314Leu Uncertain significance ★ ⚠ same residue
PRMT6 c.-8C>T Likely benign same condition
PRMT6 p.Gly12= Likely benign same condition
PRMT6 p.Leu9Val Likely benign same condition
PRMT6 p.Ala254Gly Uncertain significance ★ ⚠ same type
PRMT6 p.Ala261Pro Uncertain significance ★ ⚠ same type
PRMT6 p.Ala261Thr Uncertain significance ★ ⚠ same type
PRMT6 p.Ala315Ser 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/prmt6-p-pro314 (accessed [today's date]).

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