Is PTPRF p.Ser607= (c.1821C>T) pathogenic?

PTPRF p.Ser607= (c.1821C>T) is classified Likely benign in PTPRF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-27). Very rare (popmax 0.00268%, afr); Associated with PTPRF-related disorder.

What condition is associated with PTPRF p.Ser607= (c.1821C>T)?

PTPRF p.Ser607= (c.1821C>T) is associated with PTPRF-related disorder (ClinVar).

How common is PTPRF p.Ser607= (c.1821C>T) in the general population?

PTPRF p.Ser607= (c.1821C>T) is very rare (popmax 0.00268%, afr) (gnomAD).

PTPRF p.Ser607=

c.1821C>T · rs1318858989 · VCV3051896

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00268%, afr)

Conditions

PTPRF-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.079	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.1	GERP -4.1
Overall
CADD	12.94	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00268% African / African-American · 2/74,530 alleles

Filtering AF 0.000445% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000167%

Overall 0.000569% 9/1,582,750 alleles · very rare exomes 8/1,430,658 · genomes 1/152,092 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00268%	37,265
East Asian	0.00228%	43,930
Admixed American	0.00178%	56,138
Remaining individualsnot grpmax-eligible	0.00163%	61,298
South Asian	0.00115%	86,834
European (non-Finnish)	0.000258%	387,579

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: PTPRF
Protein: p.Ser607=
Coding: c.1821C>T
MANE Select: NM_002840
dbSNP: rs1318858989
Type: single nucleotide variant
Location: chr1:43597755 (GRCh38)
Gene constraint: LOEUF 0.348 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.43 · 13 PDB

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

Disease context

PTPRF-related disorder

Similar variants

PTPRF p.Ser607Thr Likely benign same residue
PTPRF c.3389+4T>G Likely benign same condition
PTPRF c.3974-829C>T Likely benign same condition
PTPRF c.4372-7C>T Likely benign same condition
PTPRF p.Ala157= Benign same condition
PTPRF p.Arg1286= Likely benign same condition
PTPRF p.Asn441= Likely benign same condition
PTPRF p.Asp562Asn 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/ptprf-p-ser607 (accessed [today's date]).

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