Is TEX11 p.Pro25Ser (c.73C>T) pathogenic?

TEX11 p.Pro25Ser (c.73C>T) is classified Uncertain significance in TEX11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-26). AlphaMissense: likely benign (0.1085); Very rare (popmax 0.004%, nfe); Associated with Inborn genetic diseases.

What condition is associated with TEX11 p.Pro25Ser (c.73C>T)?

TEX11 p.Pro25Ser (c.73C>T) is associated with Inborn genetic diseases (ClinVar).

How common is TEX11 p.Pro25Ser (c.73C>T) in the general population?

TEX11 p.Pro25Ser (c.73C>T) is very rare (popmax 0.004%, nfe) (gnomAD).

What do computational predictors say about TEX11 p.Pro25Ser (c.73C>T)?

AlphaMissense predicts likely benign (score 0.1085) — an in-silico prediction, not a clinical call.

TEX11 p.Pro25Ser

c.73C>T · VCV4183100

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1085 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.004%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1085	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.04	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 -0.35	GERP -2.8
Regional constraint	o/e 0.83	unconstrained · MANE · 379 kb · p 2e-05 · regional, not allelic
Overall
CADD	0.117	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 P40S vs ClinVar P25S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% European (non-Finnish) · 35/875,202 alleles

Filtering AF 0.0029% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00257%

Overall 0.00313% 37/1,181,051 alleles · very rare exomes 36/1,069,249 · genomes 1/111,802 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00431%	23,228
European (non-Finnish)grpmax	0.004%	25,006

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro25Ser
Coding: c.73C>T
MANE Select: NM_031276
Type: single nucleotide variant
Location: chrX:70880074 (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-pro25ser (accessed [today's date]).

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