Is TEX11 p.Ser511Pro (c.1531T>C) pathogenic?

TEX11 p.Ser511Pro (c.1531T>C) is classified Uncertain significance in TEX11 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-16). AlphaMissense: likely benign (0.0722); Very rare (popmax 0.00216%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TEX11 p.Ser511Pro (c.1531T>C)?

TEX11 p.Ser511Pro (c.1531T>C) is associated with Inborn genetic diseases (ClinVar).

How common is TEX11 p.Ser511Pro (c.1531T>C) in the general population?

TEX11 p.Ser511Pro (c.1531T>C) is very rare (popmax 0.00216%, nfe) (gnomAD).

What do computational predictors say about TEX11 p.Ser511Pro (c.1531T>C)?

AlphaMissense predicts likely benign (score 0.0722) — an in-silico prediction, not a clinical call.

TEX11 p.Ser511Pro

c.1531T>C · rs1220744701 · VCV3176259

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0722 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00216%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0722	likely benign
REVEL	0.01	strongly benign-leaning
SaProt	LLR -6.45	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 -1.9	GERP -3.5
Regional constraint	o/e 0.83	unconstrained · MANE · 379 kb · p 2e-05 · regional, not allelic
Overall
CADD	0.258	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S526P vs ClinVar S511P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00216% European (non-Finnish) · 19/879,409 alleles

Filtering AF 0.00138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00111%

Overall 0.0016% 19/1,189,580 alleles · very rare

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: TEX11
Protein: p.Ser511Pro
Coding: c.1531T>C
MANE Select: NM_031276
dbSNP: rs1220744701
Type: single nucleotide variant
Location: chrX:70629688 (GRCh38)
Structure: AlphaFold pLDDT 86.45

Full TEX11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TEX11 p.Ala871Val Uncertain significance ★ ⚠ same condition
TEX11 p.Ala98Ser Uncertain significance ★ ⚠ same condition
TEX11 p.Arg147Trp Uncertain significance ★ ⚠ same condition
TEX11 p.Arg474Gly Uncertain significance ★ ⚠ same condition
TEX11 p.Arg880Cys Uncertain significance ★ ⚠ same condition
TEX11 p.Asn325Lys Uncertain significance ★ ⚠ same condition
TEX11 p.Asn491Lys Conflicting classifications of pathogenicity ★ ⚠ same condition
TEX11 p.Asn504Thr Uncertain significance ★ ⚠ 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/tex11-p-ser511pro (accessed [today's date]).

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