Is ATRX p.Ser79Ter (c.236C>G) pathogenic?

ATRX p.Ser79Ter (c.236C>G) is classified Pathogenic in ATRX (ClinVar, No assertion criteria, 1 submitter; last evaluated 2003-08-01). Absent from gnomAD v4.1; Associated with alpha-thalassemia-myelodysplastic syndrome.

What condition is associated with ATRX p.Ser79Ter (c.236C>G)?

ATRX p.Ser79Ter (c.236C>G) is associated with alpha-thalassemia-myelodysplastic syndrome (ClinVar).

How common is ATRX p.Ser79Ter (c.236C>G) in the general population?

ATRX p.Ser79Ter (c.236C>G) is absent from gnomAD v4.1 (gnomAD).

How is Alpha-thalassemia-myelodysplastic syndrome inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

ATRX p.Ser79Ter

c.236C>G · rs122445107 · VCV11741

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

alpha-thalassemia-myelodysplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 35
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	phastCons 1
Overall
CADD	35.0	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

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: ATRX
Protein: p.Ser79Ter
Coding: c.236C>G
MANE Select: NM_000489
dbSNP: rs122445107
Type: single nucleotide variant
Location: chrX:77697589 (GRCh38)
Structure: AlphaFold pLDDT 52.40 · 13 PDB
Residue 79: the 'disordered' region

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

Disease context

alpha-thalassemia-myelodysplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Alpha-thalassemia-myelodysplastic syndrome (Orphanet):

Inheritance: Not applicable
Onset: Adult

Similar variants

ATRX p.Arg246Cys Pathogenic/Likely pathogenic ★★ same condition
ATRX p.Arg37Ter Pathogenic/Likely pathogenic ★★ same condition
ATRX p.Tyr1847Cys Likely pathogenic ★★ same condition
ATRX c.6326+3A>G Uncertain significance ★★ same condition
ATRX p.Arg160His Uncertain significance ★★ ⚠ same condition
ATRX p.Gln689Arg Uncertain significance ★★ ⚠ same condition
ATRX p.Lys1357Arg Uncertain significance ★★ ⚠ same condition
ATRX p.Lys796Asn 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/atrx-p-ser79ter (accessed [today's date]).

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