Is PCNT p.Arg1903Phe (c.5707_5708delinsTT) pathogenic?

PCNT p.Arg1903Phe (c.57075708delinsTT) is classified Uncertain significance in PCNT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-22). No gnomAD frequency available for this variant; Associated with microcephalic osteodysplastic primordial dwarfism type II.

What condition is associated with PCNT p.Arg1903Phe (c.5707_5708delinsTT)?

PCNT p.Arg1903Phe (c.5707_5708delinsTT) is associated with microcephalic osteodysplastic primordial dwarfism type II (ClinVar).

How common is PCNT p.Arg1903Phe (c.5707_5708delinsTT) in the general population?

PCNT p.Arg1903Phe (c.5707_5708delinsTT) is no gnomAD frequency available for this variant (gnomAD).

PCNT p.Arg1903Phe

c.5707_5708delinsTT · rs2147674617 · VCV1336729

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microcephalic osteodysplastic primordial dwarfism type II

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.5	GERP -5.1
Regional constraint	o/e 1.03	unconstrained · MANE · 121 kb · p 0.027 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: PCNT
Protein: p.Arg1903Phe
Coding: c.5707_5708delinsTT
MANE Select: NM_006031
dbSNP: rs2147674617
Type: Indel
Location: chr21:46411780 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)

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

Disease context

microcephalic osteodysplastic primordial dwarfism type II — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PCNT p.Arg1903Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
PCNT p.Arg1903Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
PCNT p.Arg1903= Likely benign ★★ same residue
PCNT p.Val719_Lys720delinsPheAsnThrIleTer Likely pathogenic ★ same condition
PCNT p.Arg1903His Conflicting classifications of pathogenicity ★ ⚠ same residue
PCNT c.1032+1G>A Pathogenic/Likely pathogenic ★★ same condition
PCNT c.1680-1G>C Likely pathogenic ★★ same condition
PCNT c.2155-21_2186del Likely pathogenic ★★ 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-arg1903phe (accessed [today's date]).

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