Is PCNT p.Gln1908= (c.5724G>A) pathogenic?

PCNT p.Gln1908= (c.5724G>A) is classified Benign/Likely benign in PCNT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-29). Rare (popmax 0.627%, eas); Associated with microcephalic osteodysplastic primordial dwarfism type II.

What condition is associated with PCNT p.Gln1908= (c.5724G>A)?

PCNT p.Gln1908= (c.5724G>A) is associated with microcephalic osteodysplastic primordial dwarfism type II (ClinVar).

How common is PCNT p.Gln1908= (c.5724G>A) in the general population?

PCNT p.Gln1908= (c.5724G>A) is rare (popmax 0.627%, eas) (gnomAD).

PCNT p.Gln1908=

c.5724G>A · rs199519762 · VCV897512

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.627%, eas)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.4	GERP 1.5, phastCons 0.83
Overall
CADD	2.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.627% East Asian · 278/44,348 alleles

Filtering AF 0.566% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.543%

Overall 0.0176% 281/1,594,698 alleles · rare exomes 261/1,442,348 · genomes 20/152,350 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.627%	160
Remaining individualsnot grpmax-eligible	0.00485%	20,613

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.Gln1908=
Coding: c.5724G>A
MANE Select: NM_006031
dbSNP: rs199519762
Type: single nucleotide variant
Location: chr21:46411797 (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.Gln1908Lys Uncertain significance ★ ⚠ same residue
PCNT c.1032+1G>A Pathogenic/Likely pathogenic ★★ same condition
PCNT c.1680-1G>C Likely pathogenic ★★ same condition
PCNT c.5995-2A>C Likely pathogenic ★★ same condition
PCNT c.7024+1G>C Likely pathogenic ★★ same condition
PCNT c.7691-1G>A Likely pathogenic ★★ same condition
PCNT c.9624-2A>G Likely pathogenic ★★ same condition
PCNT p.Arg1730Ter Pathogenic/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-gln1908 (accessed [today's date]).

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