Is PRRX1 p.Ser67= (c.201G>T) pathogenic?

PRRX1 p.Ser67= (c.201G>T) is classified Likely benign in PRRX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-04). Very rare (popmax 0.00134%, afr).

How common is PRRX1 p.Ser67= (c.201G>T) in the general population?

PRRX1 p.Ser67= (c.201G>T) is very rare (popmax 0.00134%, afr) (gnomAD).

PRRX1 p.Ser67=

c.201G>T · rs1005904543 · VCV728818

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 0.39	GERP -4, phastCons 0.98
Overall
CADD	8.852	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,880 alleles

Overall 6.21e-05% 1/1,610,230 alleles · very rare exomes 0/1,458,032 · genomes 1/152,198 · joint denominator

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: PRRX1
Protein: p.Ser67=
Coding: c.201G>T
MANE Select: NM_022716
dbSNP: rs1005904543
Type: single nucleotide variant
Location: chr1:170664419 (GRCh38)
Gene constraint: LOEUF 0.571 · pLI 0.89 (gnomAD)
Structure: AlphaFold pLDDT 66.38
Residue 67: the 'disordered' region

Full PRRX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRRX1 p.Arg62Gln Benign ★★ same type
PRRX1 p.Leu70= Likely benign ★★ same type
PRRX1 p.Ser104Gly Benign/Likely benign ★★ same type
PRRX1 p.Arg124Ter Pathogenic ★ same type
PRRX1 c.418-1G>A Uncertain significance ★ same type
PRRX1 c.-13G>T Uncertain significance ★ same type
PRRX1 p.Ala158Thr Uncertain significance ★ same type
PRRX1 p.Ala184Thr Uncertain significance ★ ⚠ same type

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/prrx1-p-ser67 (accessed [today's date]).

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