Is TEX14 p.Pro893Arg (c.2678C>G) pathogenic?

TEX14 p.Pro893Arg (c.2678C>G) is classified Uncertain significance in TEX14 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-22). AlphaMissense: likely benign (0.0851); Absent from gnomAD v4.1; Associated with spermatogenic failure 23.

What condition is associated with TEX14 p.Pro893Arg (c.2678C>G)?

TEX14 p.Pro893Arg (c.2678C>G) is associated with spermatogenic failure 23 (ClinVar).

How common is TEX14 p.Pro893Arg (c.2678C>G) in the general population?

TEX14 p.Pro893Arg (c.2678C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TEX14 p.Pro893Arg (c.2678C>G)?

AlphaMissense predicts likely benign (score 0.0851) — an in-silico prediction, not a clinical call.

TEX14 p.Pro893Arg

c.2678C>G · VCV3731521

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0851 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

spermatogenic failure 23

Computational evidence

Protein change
AlphaMissense	0.0851	likely benign
REVEL	0.091	moderately benign-leaning
SaProt	LLR -6.56	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 1.1	GERP 0.59, phastCons 0.002
Regional constraint	o/e 0.88	unconstrained · MANE · 45 kb · p 6e-05 · regional, not allelic
Overall
CADD	9.275	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 P899R vs ClinVar P893R) — verify the residue.

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: TEX14
Protein: p.Pro893Arg
Coding: c.2678C>G
MANE Select: NM_031272
Type: single nucleotide variant
Location: chr17:58587920 (GRCh38)
Gene constraint: LOEUF 1.043 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.95 · 2 PDB

Full TEX14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TEX14 p.Arg1218Ter Likely pathogenic ★ same condition
TEX14 p.Trp981Ter Likely pathogenic ★ same condition
TEX14 c.2576+2T>G Uncertain significance ★ same condition
TEX14 c.3818-1G>A Conflicting classifications of pathogenicity ★ same condition
TEX14 p.Ala64Val Uncertain significance ★ ⚠ same condition
TEX14 p.Arg335Ter Conflicting classifications of pathogenicity ★ same condition
TEX14 p.Gln237Glu Conflicting classifications of pathogenicity ★ ⚠ same condition
TEX14 p.Arg85Leu Pathogenic ⚠ 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/tex14-p-pro893arg (accessed [today's date]).

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