Is TEX14 p.Ser1209fs (c.3625_3628del) pathogenic?

TEX14 p.Ser1209fs (c.36253628del) is classified Pathogenic in TEX14 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-23). Ultra-rare (popmax 0.0376%, nfe); Associated with Non-obstructive azoospermia.

What condition is associated with TEX14 p.Ser1209fs (c.3625_3628del)?

TEX14 p.Ser1209fs (c.3625_3628del) is associated with Non-obstructive azoospermia (ClinVar).

How common is TEX14 p.Ser1209fs (c.3625_3628del) in the general population?

TEX14 p.Ser1209fs (c.3625_3628del) is ultra-rare (popmax 0.0376%, nfe) (gnomAD).

TEX14 p.Ser1209fs

c.3625_3628del · rs553754986 · VCV1244237

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0376%, nfe)

Conditions

Non-obstructive azoospermia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 24 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.7	GERP -2.2, phastCons 1
Overall
CADD	27.9	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0376% European (non-Finnish) · 444/1,180,006 alleles

Filtering AF 0.0347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0336%

Overall 0.0287% 464/1,614,030 alleles · ultra-rare exomes 432/1,461,848 · genomes 32/152,182 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0376%	2,658
Remaining individualsnot grpmax-eligible	0.0192%	5,207
African / African-American	0.004%	24,974
Admixed American	0.00333%	29,999
South Asian	0.0022%	45,544
Finnishnot grpmax-eligible	0.00156%	64,040

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: TEX14
Protein: p.Ser1209fs
Coding: c.3625_3628del
MANE Select: NM_031272
dbSNP: rs553754986
Type: Deletion
Location: chr17:58572010 (GRCh38)
Gene constraint: LOEUF 1.043 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.95 · 2 PDB
Residue 1209: a UniProt-annotated variant site (in spgf23)

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

Disease context

Non-obstructive azoospermia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TEX14 p.Pro1161fs Pathogenic ★ same condition
TEX14 p.Ser1209Cys Uncertain significance ★ ⚠ same residue
TEX14 p.Cys1183Ter Pathogenic ★ same condition
TEX14 p.Gln982Ter Pathogenic ★ same condition
TEX14 p.Leu497Pro Likely pathogenic ★ same condition
TEX14 p.Tyr1056Ter Pathogenic ★ same condition
TEX14 p.Asn83His Uncertain significance ★ ⚠ same condition
TEX14 p.Gln1369Pro 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/tex14-p-ser1209fs (accessed [today's date]).

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