Is PTPRT p.Asp683= (c.2049C>T) pathogenic?

PTPRT p.Asp683= (c.2049C>T) is classified Likely benign in PTPRT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Very rare (popmax 0.00134%, afr); Associated with PTPRT-related disorder.

What condition is associated with PTPRT p.Asp683= (c.2049C>T)?

PTPRT p.Asp683= (c.2049C>T) is associated with PTPRT-related disorder (ClinVar).

How common is PTPRT p.Asp683= (c.2049C>T) in the general population?

PTPRT p.Asp683= (c.2049C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

PTPRT p.Asp683=

c.2049C>T · rs367646009 · VCV3047530

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 3.9	GERP 2.7, phastCons 1
Overall
CADD	8.105	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,894 alleles

Overall 6.2e-05% 1/1,613,922 alleles · very rare exomes 0/1,461,820 · genomes 1/152,102 · 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: PTPRT
Protein: p.Asp683=
Coding: c.2049C>T
MANE Select: NM_007050
dbSNP: rs367646009
Type: single nucleotide variant
Location: chr20:42315813 (GRCh38)
Gene constraint: LOEUF 0.395 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 83.99 · 1 PDB
Residue 683: the fibronectin type-iii 4 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-asp683 (accessed [today's date]).

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