Is PRKX p.Asp327= (c.981C>T) pathogenic?

PRKX p.Asp327= (c.981C>T) is classified Benign in PRKX (ClinVar, Multiple submitters, 2 submitters; last evaluated 2017-11-24). Low-frequency (popmax 1.05%, afr).

How common is PRKX p.Asp327= (c.981C>T) in the general population?

PRKX p.Asp327= (c.981C>T) is low-frequency (popmax 1.05%, afr) (gnomAD).

PRKX p.Asp327=

c.981C>T · rs146727237 · VCV788046

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.05%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -2.4
Overall
CADD	0.223	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.05% African / African-American · 598/56,906 alleles

Filtering AF 0.981% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.953%

Overall 0.0638% 771/1,208,213 alleles · low-frequency exomes 421/1,097,195 · genomes 350/111,018 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.05%	95
Remaining individualsnot grpmax-eligible	0.156%	643
Admixed American	0.0946%	1,057
Middle Eastern	0.092%	1,087
European (non-Finnish)	0.00537%	18,638
South Asian	0.00531%	18,835
Finnishnot grpmax-eligible	0.00216%	46,397

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: PRKX
Protein: p.Asp327=
Coding: c.981C>T
MANE Select: NM_005044
dbSNP: rs146727237
Type: single nucleotide variant
Location: chrX:3612296 (GRCh38)
Structure: AlphaFold pLDDT 89.71
Residue 327: the agc-kinase c-terminal domain

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

Similar variants

PRKX c.951+10A>T Benign ★★ same type
PRKX c.952-9G>A Benign ★★ same type
PRKX p.Ala258Gly Uncertain significance ★ ⚠ same type
PRKX p.Ala345Val Uncertain significance ★ ⚠ same type
PRKX p.Ala76Thr Uncertain significance ★ ⚠ same type
PRKX p.Arg120Cys Uncertain significance ★ ⚠ same type
PRKX p.Arg139His Uncertain significance ★ ⚠ same type
PRKX p.Arg141Trp 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/prkx-p-asp327 (accessed [today's date]).

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