Is DPRX p.Arg156Ter (c.466C>T) pathogenic?

DPRX p.Arg156Ter (c.466C>T) is classified Pathogenic in DPRX (ClinVar, No assertion criteria, 1 submitter; last evaluated 2001-11-18). Rare (popmax 0.28%, mid); Associated with Short stature.

What condition is associated with DPRX p.Arg156Ter (c.466C>T)?

DPRX p.Arg156Ter (c.466C>T) is associated with Short stature (ClinVar).

How common is DPRX p.Arg156Ter (c.466C>T) in the general population?

DPRX p.Arg156Ter (c.466C>T) is rare (popmax 0.28%, mid) (gnomAD).

DPRX p.Arg156Ter

c.466C>T · rs201435914 · VCV599534

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.28%, mid)

Conditions

Short stature

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
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.81	GERP -2.2, phastCons 0.017
Overall
CADD	36.0	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

Grpmax group 0.28% Middle Eastern · 17/6,062 alleles

Filtering AF 0.179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.147%

Overall 0.0359% 579/1,614,152 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.28%	357
Admixed American	0.0767%	1,304
Remaining individualsnot grpmax-eligible	0.0464%	2,155
European (non-Finnish)	0.0385%	2,599
Ashkenazi Jewishnot grpmax-eligible	0.0203%	4,935
South Asian	0.0176%	5,692
African / African-American	0.00933%	10,720
East Asian	0.00446%	22,442
Finnishnot grpmax-eligible	0.00312%	32,015

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: DPRX
Protein: p.Arg156Ter
Coding: c.466C>T
MANE Select: NM_001012728
dbSNP: rs201435914
Type: single nucleotide variant
Location: chr19:53636878 (GRCh38)
Gene constraint: LOEUF 1.777 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.08

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

Disease context

Short stature — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPRX p.Arg156Gln Likely benign ★ same residue
DPRX p.Ala104Glu Uncertain significance ★ ⚠ same type
DPRX p.Ala173Thr Uncertain significance ★ ⚠ same type
DPRX p.Arg189Gln Uncertain significance ★ ⚠ same type
DPRX p.Arg189Gly Uncertain significance ★ ⚠ same type
DPRX p.Arg8Cys Uncertain significance ★ ⚠ same type
DPRX p.Asn103Asp Uncertain significance ★ ⚠ same type
DPRX p.Asn112Asp 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/dprx-p-arg156ter (accessed [today's date]).

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