Is PTPRQ p.Ser2008= (c.6024G>A) pathogenic?

PTPRQ p.Ser2008= (c.6024G>A) is classified Uncertain significance in PTPRQ (ClinVar, Single submitter, 1 submitter; last evaluated 2020-09-30). Very rare (popmax 0.00491%, eas); Associated with sensorineural hearing loss disorder.

What condition is associated with PTPRQ p.Ser2008= (c.6024G>A)?

PTPRQ p.Ser2008= (c.6024G>A) is associated with sensorineural hearing loss disorder (ClinVar).

How common is PTPRQ p.Ser2008= (c.6024G>A) in the general population?

PTPRQ p.Ser2008= (c.6024G>A) is very rare (popmax 0.00491%, eas) (gnomAD).

PTPRQ p.Ser2008=

c.6024G>A · rs1238341806 · VCV984394

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00491%, eas)

Conditions

sensorineural hearing loss disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.409	indeterminate
Splicing
SpliceAI	Δ0.78	donor loss · deltas
Pangolin	Δ0.68	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Overall
CADD	19.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00491% East Asian · 2/40,760 alleles

Filtering AF 0.000813% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000304%

Overall 0.000452% 7/1,547,330 alleles · very rare exomes 5/1,395,244 · genomes 2/152,086 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00491%	20,380
Admixed American	0.00395%	25,294
European (non-Finnish)	0.000262%	381,569

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: PTPRQ
Protein: p.Ser2008=
Coding: c.6024G>A
MANE Select: NM_001145026
dbSNP: rs1238341806
Type: single nucleotide variant
Location: chr12:80649669 (GRCh38)
Gene constraint: LOEUF 0.941 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.35 · 1 PDB

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

Disease context

sensorineural hearing loss disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PTPRQ c.1359+2T>C Pathogenic/Likely pathogenic ★★ same type
PTPRQ c.6024+2T>C Pathogenic ★★ same type
PTPRQ c.6025-1G>A Pathogenic/Likely pathogenic ★★ same type
PTPRQ c.6327+1G>A Likely pathogenic ★★ same type
PTPRQ p.Arg1747Ter Pathogenic/Likely pathogenic ★★ same type
PTPRQ p.Arg2159Ter Pathogenic ★★ same type
PTPRQ p.Gln1336Ter Pathogenic ★★ same type
PTPRQ p.Ser874Ter Likely pathogenic ★★ 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/ptprq-p-ser2008 (accessed [today's date]).

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