Is DMRT2 p.Asp43fs (c.129del) pathogenic?

DMRT2 p.Asp43fs (c.129del) is classified Likely pathogenic in DMRT2 (ClinVar, Single submitter, 2 submitters). Associated with spondylocostal dysostosis 7, autosomal recessive.

What condition is associated with DMRT2 p.Asp43fs (c.129del)?

DMRT2 p.Asp43fs (c.129del) is associated with spondylocostal dysostosis 7, autosomal recessive (ClinVar).

DMRT2 p.Asp43fs

c.129del · VCV3900977

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

spondylocostal dysostosis 7, autosomal recessive

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 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.3	GERP -0.63, phastCons 0.87
Region caveats
Repeat context	tandem	(GAC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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

Variant & gene context

Gene: DMRT2
Protein: p.Asp43fs
Coding: c.129del
MANE Select: NM_181872
Type: Deletion
Location: chr9:1051742 (GRCh38)
Gene constraint: LOEUF 1.279 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.37
Residue 43: the 'disordered' region

Full DMRT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spondylocostal dysostosis 7, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DMRT2 p.Asp43Ala Uncertain significance ★ ⚠ same residue
DMRT2 p.Asp43Asn Uncertain significance ★ ⚠ same residue
DMRT2 p.Asp43Val Uncertain significance ★ ⚠ same residue
DMRT2 p.Arg81fs Uncertain significance ★ same type
DMRT2 p.Ser206fs Uncertain significance ★ same type

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/dmrt2-p-asp43fs (accessed [today's date]).

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