Is PIGN p.Pro609= (c.1827G>A) pathogenic?

PIGN p.Pro609= (c.1827G>A) is classified Likely benign in PIGN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-05). Ultra-rare (popmax 0.0333%, mid); Associated with multiple congenital anomalies-hypotonia-seizures syndrome 1.

What condition is associated with PIGN p.Pro609= (c.1827G>A)?

PIGN p.Pro609= (c.1827G>A) is associated with multiple congenital anomalies-hypotonia-seizures syndrome 1 (ClinVar).

How common is PIGN p.Pro609= (c.1827G>A) in the general population?

PIGN p.Pro609= (c.1827G>A) is ultra-rare (popmax 0.0333%, mid) (gnomAD).

PIGN p.Pro609=

c.1827G>A · rs750102703 · VCV1058813

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, mid)

Conditions

multiple congenital anomalies-hypotonia-seizures syndrome 1

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
Pangolin	Δ0.23	loss · gain 0.05 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.75	GERP -4.2, phastCons 0.96
Overall
CADD	12.35	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% Middle Eastern · 2/6,004 alleles

Filtering AF 0.0129% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0105%

Overall 0.00154% 24/1,553,540 alleles · ultra-rare exomes 23/1,401,394 · genomes 1/152,146 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0333%	3,002
South Asian	0.0202%	4,947
Remaining individualsnot grpmax-eligible	0.00166%	60,218
European (non-Finnish)	0.000349%	286,823

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: PIGN
Protein: p.Pro609=
Coding: c.1827G>A
MANE Select: NM_176787
dbSNP: rs750102703
Type: single nucleotide variant
Location: chr18:62105575 (GRCh38)
Gene constraint: LOEUF 1.46 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.33

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

Disease context

multiple congenital anomalies-hypotonia-seizures syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PIGN p.Pro609Leu Uncertain significance ★★ same residue
PIGN c.1251+1G>A Pathogenic/Likely pathogenic ★★ same condition
PIGN c.1252-2A>G Pathogenic/Likely pathogenic ★★ same condition
PIGN c.1434+5G>A Pathogenic/Likely pathogenic ★★ same condition
PIGN c.1574+1G>A Likely pathogenic ★★ same condition
PIGN c.1674+1G>A Likely pathogenic ★★ same condition
PIGN c.1674+1G>C Pathogenic ★★ same condition
PIGN c.1675-1G>T 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/pign-p-pro609 (accessed [today's date]).

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