Is PCNT p.Arg3208= (c.9624A>G) pathogenic?

PCNT p.Arg3208= (c.9624A>G) is classified Likely benign in PCNT (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-06). Very rare (popmax 0.000515%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PCNT p.Arg3208= (c.9624A>G)?

PCNT p.Arg3208= (c.9624A>G) is associated with Inborn genetic diseases (ClinVar).

How common is PCNT p.Arg3208= (c.9624A>G) in the general population?

PCNT p.Arg3208= (c.9624A>G) is very rare (popmax 0.000515%, nfe) (gnomAD).

PCNT p.Arg3208=

c.9624A>G · VCV4861677

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000515%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.064	moderately benign-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.29 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.24	phastCons 0.69
Overall
CADD	4.073	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000515% European (non-Finnish) · 6/1,164,566 alleles

Filtering AF 0.000185% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000122%

Overall 0.000376% 6/1,595,964 alleles · very rare exomes 6/1,445,044 · genomes 0/150,920 · joint denominator

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: PCNT
Protein: p.Arg3208=
Coding: c.9624A>G
MANE Select: NM_006031
Type: single nucleotide variant
Location: chr21:46442497 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)
Residue 3208: the 'calmodulin-binding' region; the 'interaction with nek2' region

Full PCNT 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

PCNT p.Arg3208Ser Uncertain significance ★ ⚠ same residue
PCNT p.Gln910Ter Pathogenic ★★ same condition
PCNT p.Ala1194Val Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1400Thr Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1457Val Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1827Ser Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1827Thr Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1831Val 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/pcnt-p-arg3208 (accessed [today's date]).

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