Is PRKCD p.Ala455= (c.1365T>G) pathogenic?

PRKCD p.Ala455= (c.1365T>G) is classified Likely benign in PRKCD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-29). Absent from gnomAD v4.1.

How common is PRKCD p.Ala455= (c.1365T>G) in the general population?

PRKCD p.Ala455= (c.1365T>G) is absent from gnomAD v4.1 (gnomAD).

PRKCD p.Ala455=

c.1365T>G · rs1575543080 · VCV747735

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,708)

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 -7.2	GERP -5.2
Overall
CADD	0.952	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,708). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRKCD
Protein: p.Ala455=
Coding: c.1365T>G
MANE Select: NM_006254
dbSNP: rs1575543080
Type: single nucleotide variant
Location: chr3:53187352 (GRCh38)
Gene constraint: LOEUF 0.344 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 81.29 · 2 PDB
Residue 455: the protein kinase domain

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

Similar variants

PRKCD c.787+4C>T Uncertain significance ★★ same type
PRKCD p.Ala195Val Uncertain significance ★★ ⚠ same type
PRKCD p.Ala212Val Uncertain significance ★★ ⚠ same type
PRKCD p.Ala404Gly Uncertain significance ★★ ⚠ same type
PRKCD p.Ala454Thr Uncertain significance ★★ same type
PRKCD p.Arg273Trp Uncertain significance ★★ ⚠ same type
PRKCD p.Arg40His Uncertain significance ★★ same type
PRKCD p.Arg444Cys 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/prkcd-p-ala455 (accessed [today's date]).

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