Is PRRX1 p.Ser200= (c.600C>T) pathogenic?

PRRX1 p.Ser200= (c.600C>T) is classified Likely benign in PRRX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-05). Ultra-rare (popmax 0.0198%, sas); Associated with Inborn genetic diseases.

What condition is associated with PRRX1 p.Ser200= (c.600C>T)?

PRRX1 p.Ser200= (c.600C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PRRX1 p.Ser200= (c.600C>T) in the general population?

PRRX1 p.Ser200= (c.600C>T) is ultra-rare (popmax 0.0198%, sas) (gnomAD).

PRRX1 p.Ser200=

c.600C>T · rs151333816 · VCV3219785

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0198%, sas)

Conditions

Inborn genetic diseases

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 0.86	GERP -0.43, phastCons 1
Overall
CADD	15.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0198% South Asian · 18/91,086 alleles

Filtering AF 0.0127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.00669% 108/1,613,862 alleles · ultra-rare exomes 102/1,461,662 · genomes 6/152,200 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0198%	5,060
Remaining individualsnot grpmax-eligible	0.0176%	5,679
Admixed American	0.01%	9,999
Ashkenazi Jewishnot grpmax-eligible	0.00676%	14,800
European (non-Finnish)	0.00602%	16,618

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.Ser200=
Coding: c.600C>T
MANE Select: NM_022716
dbSNP: rs151333816
Type: single nucleotide variant
Location: chr1:170736048 (GRCh38)
Gene constraint: LOEUF 0.571 · pLI 0.89 (gnomAD)
Structure: AlphaFold pLDDT 66.38

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRRX1 p.Ser200Arg Likely benign same residue
PRRX1 p.Ala158Thr Uncertain significance ★ same condition
PRRX1 p.Ala184Thr Uncertain significance ★ ⚠ same condition
PRRX1 p.Ala201Thr Uncertain significance ★ ⚠ same condition
PRRX1 p.Ala30Glu Uncertain significance ★ ⚠ same condition
PRRX1 p.Arg11Trp Uncertain significance ★ ⚠ same condition
PRRX1 p.Gln240His Uncertain significance ★ ⚠ same condition
PRRX1 p.Gly17Ser 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/prrx1-p-ser200 (accessed [today's date]).

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