Is PRMT7 p.Phe583fs (c.1727_1745dup) pathogenic?

PRMT7 p.Phe583fs (c.17271745dup) is classified Likely pathogenic in PRMT7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-24). Associated with short stature-brachydactyly-obesity-global developmental delay syndrome.

What condition is associated with PRMT7 p.Phe583fs (c.1727_1745dup)?

PRMT7 p.Phe583fs (c.1727_1745dup) is associated with short stature-brachydactyly-obesity-global developmental delay syndrome (ClinVar).

PRMT7 p.Phe583fs

c.1727_1745dup · VCV4277453

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

short stature-brachydactyly-obesity-global developmental delay syndrome

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 17 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.85	GERP -4.8, phastCons 0.21

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

Variant & gene context

Gene: PRMT7
Protein: p.Phe583fs
Coding: c.1727_1745dup
MANE Select: NM_019023
Type: Duplication
Location: chr16:68355798 (GRCh38)
Gene constraint: LOEUF 1.01 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.19
Residue 583: the sam-dependent mtase prmt-type 2 domain

Full PRMT7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

short stature-brachydactyly-obesity-global developmental delay syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRMT7 p.Val416fs Pathogenic ★★ same condition
PRMT7 p.Asp501fs Likely pathogenic ★ same condition
PRMT7 p.Glu153fs Likely pathogenic ★ same condition
PRMT7 p.His447Ter Likely pathogenic ★ same condition
PRMT7 p.Leu448fs Likely pathogenic ★ same condition
PRMT7 c.1056-1G>T Pathogenic/Likely pathogenic ★★ same condition
PRMT7 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same condition
PRMT7 p.Arg390Ter 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/prmt7-p-phe583fs (accessed [today's date]).

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