Is MAPT p.Arg23Ser (c.69G>C) pathogenic?

MAPT p.Arg23Ser (c.69G>C) is classified Uncertain significance in MAPT (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.2534); Absent from gnomAD v4.1; Associated with prostate cancer.

What condition is associated with MAPT p.Arg23Ser (c.69G>C)?

MAPT p.Arg23Ser (c.69G>C) is associated with prostate cancer (ClinVar).

How common is MAPT p.Arg23Ser (c.69G>C) in the general population?

MAPT p.Arg23Ser (c.69G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAPT p.Arg23Ser (c.69G>C)?

AlphaMissense predicts likely benign (score 0.2534) — an in-silico prediction, not a clinical call.

MAPT p.Arg23Ser

c.69G>C · rs193920967 · VCV161704

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2534 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

prostate cancer

Computational evidence

Protein change
AlphaMissense	0.2534	likely benign
REVEL	0.211	benign-leaning
SaProt	LLR -4.79	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 2.8, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 29 kb · p 0.0043 · regional, not allelic
Overall
CADD	20.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MAPT
Protein: p.Arg23Ser
Coding: c.69G>C
MANE Select: NM_001377265
dbSNP: rs193920967
Type: single nucleotide variant
Location: chr17:45962406 (GRCh38)
Gene constraint: LOEUF 0.723 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 49.56 · 299 PDB
Residue 23: the 'disordered' region

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

Disease context

prostate cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAPT p.Asp34Tyr Uncertain significance ⚠ same condition
MAPT p.Glu353Asp Uncertain significance ⚠ same condition
MAPT c.1999-10G>T Pathogenic ★★ same type
MAPT c.2091+16C>T Pathogenic ★★ same type
MAPT c.2091+3G>A Pathogenic ★★ same type
MAPT p.Arg798Trp Pathogenic ★★ ⚠ same type
MAPT p.Asn671Lys Pathogenic ★★ ⚠ same type
MAPT p.Asn688= 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/mapt-p-arg23ser (accessed [today's date]).

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