Is PRSS12 p.Pro59= (c.177G>A) pathogenic?

PRSS12 p.Pro59= (c.177G>A) is classified Uncertain significance in PRSS12 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.195%, mid); Associated with intellectual disability, autosomal recessive 1.

What condition is associated with PRSS12 p.Pro59= (c.177G>A)?

PRSS12 p.Pro59= (c.177G>A) is associated with intellectual disability, autosomal recessive 1 (ClinVar).

How common is PRSS12 p.Pro59= (c.177G>A) in the general population?

PRSS12 p.Pro59= (c.177G>A) is rare (popmax 0.195%, mid) (gnomAD).

PRSS12 p.Pro59=

c.177G>A · rs746966869 · VCV899735

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.195%, mid)

Conditions

intellectual disability, autosomal recessive 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
Constraint at this position
Conservation	phyloP -0.72	GERP -1.2
Overall
CADD	6.567	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.195% Middle Eastern · 11/5,654 alleles

Filtering AF 0.109% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0844%

Overall 0.00371% 56/1,508,128 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.195%	514
African / African-American	0.0129%	7,761
Admixed American	0.00856%	11,683
Remaining individualsnot grpmax-eligible	0.0069%	14,491
South Asian	0.00375%	26,699
European (non-Finnish)	0.00222%	45,001

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: PRSS12
Protein: p.Pro59=
Coding: c.177G>A
MANE Select: NM_003619
dbSNP: rs746966869
Type: single nucleotide variant
Location: chr4:118352544 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.42
Residue 59: the 'disordered' region

Full PRSS12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal recessive 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRSS12 c.2320+6G>C Uncertain significance ★★ same condition
PRSS12 c.821-1G>A Uncertain significance ★★ same condition
PRSS12 c.*1615C>T Uncertain significance ★★ same condition
PRSS12 c.*221A>T Uncertain significance ★★ same condition
PRSS12 p.Ala547Asp Uncertain significance ★★ ⚠ same condition
PRSS12 p.Ala79Pro Uncertain significance ★★ ⚠ same condition
PRSS12 p.Arg292Trp Uncertain significance ★★ ⚠ same condition
PRSS12 p.Arg426Gln 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/prss12-p-pro59 (accessed [today's date]).

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