Is PRR12 p.Pro1471= (c.4413T>C) pathogenic?

PRR12 p.Pro1471= (c.4413T>C) is classified Likely benign in PRR12 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-03-30). Very rare (popmax 0.00497%, nfe); Associated with PRR12-related disorder.

What condition is associated with PRR12 p.Pro1471= (c.4413T>C)?

PRR12 p.Pro1471= (c.4413T>C) is associated with PRR12-related disorder (ClinVar).

How common is PRR12 p.Pro1471= (c.4413T>C) in the general population?

PRR12 p.Pro1471= (c.4413T>C) is very rare (popmax 0.00497%, nfe) (gnomAD).

PRR12 p.Pro1471=

c.4413T>C · rs1412489213 · VCV3032455

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00497%, nfe)

Conditions

PRR12-related disorder

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 -7.2	GERP -1.5
Overall
CADD	2.648	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00497% European (non-Finnish) · 54/1,087,558 alleles

Filtering AF 0.00389% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00348%

Overall 0.00391% 57/1,457,080 alleles · very rare exomes 49/1,331,218 · genomes 8/125,862 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00497%	20,140
Finnishnot grpmax-eligible	0.00187%	53,490
Remaining individualsnot grpmax-eligible	0.00178%	56,170
African / African-American	0.00162%	61,752

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: PRR12
Protein: p.Pro1471=
Coding: c.4413T>C
MANE Select: NM_020719
dbSNP: rs1412489213
Type: single nucleotide variant
Location: chr19:49601558 (GRCh38)
Gene constraint: LOEUF 0.18 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.84
Residue 1471: the 'disordered' region; a UniProt-annotated variant site (in noc1)

Full PRR12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PRR12-related disorder

Similar variants

PRR12 p.Gln1274Ter Likely pathogenic ★ same condition
PRR12 p.Arg361Gln Uncertain significance ★ ⚠ same condition
PRR12 p.Glu1105Gly Uncertain significance ★ ⚠ same condition
PRR12 p.Gly1356Arg Uncertain significance ★ ⚠ same condition
PRR12 p.Gly369Trp Uncertain significance ★ ⚠ same condition
PRR12 p.Leu553Val Uncertain significance ★ ⚠ same condition
PRR12 p.Pro1515Arg Uncertain significance ★ ⚠ same condition
PRR12 p.Ser484Arg 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/prr12-p-pro1471 (accessed [today's date]).

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