Is PTPRT p.Phe34= (c.102T>C) pathogenic?

PTPRT p.Phe34= (c.102T>C) is classified Benign in PTPRT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-28). Rare (popmax 0.829%, sas); Associated with PTPRT-related disorder.

What condition is associated with PTPRT p.Phe34= (c.102T>C)?

PTPRT p.Phe34= (c.102T>C) is associated with PTPRT-related disorder (ClinVar).

How common is PTPRT p.Phe34= (c.102T>C) in the general population?

PTPRT p.Phe34= (c.102T>C) is rare (popmax 0.829%, sas) (gnomAD).

PTPRT p.Phe34=

c.102T>C · rs569918568 · VCV3039069

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.829%, sas)

Conditions

PTPRT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.9	GERP -0.91, phastCons 1
Overall
CADD	8.132	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.829% South Asian · 753/90,872 alleles

Filtering AF 0.78% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.76%

Overall 0.0493% 792/1,607,870 alleles · rare exomes 749/1,455,640 · genomes 43/152,230 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.829%	121
Remaining individualsnot grpmax-eligible	0.0499%	2,002
East Asian	0.00224%	44,660
Admixed American	0.00167%	59,796
European (non-Finnish)	0.00051%	195,977

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: PTPRT
Protein: p.Phe34=
Coding: c.102T>C
MANE Select: NM_007050
dbSNP: rs569918568
Type: single nucleotide variant
Location: chr20:42885919 (GRCh38)
Gene constraint: LOEUF 0.395 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.99 · 1 PDB
Residue 34: the mam domain

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

Disease context

PTPRT-related disorder

Similar variants

PTPRT p.Arg1358Pro Uncertain significance ★ ⚠ same condition
PTPRT p.Gly232Ser Uncertain significance ★ ⚠ same condition
PTPRT p.Gly274Val Uncertain significance ★ ⚠ same condition
PTPRT p.Val735Met Uncertain significance ★ ⚠ same condition
PTPRT p.Gln1366Leu Uncertain significance ⚠ same condition
PTPRT c.1154-10T>C Benign same condition
PTPRT c.2683-9G>T Benign same condition
PTPRT c.3099+10T>C Benign 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/ptprt-p-phe34 (accessed [today's date]).

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