Is PUS7 p.Phe101fs (c.303del) pathogenic?

PUS7 p.Phe101fs (c.303del) is classified Likely pathogenic in PUS7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-28). Ultra-rare (gnomAD MAF 6.705e-06); Associated with intellectual developmental disorder with abnormal behavior, microcephaly, and short stature.

How common is PUS7 p.Phe101fs (c.303del) in the general population?

PUS7 p.Phe101fs (c.303del) is ultra-rare (gnomAD MAF 6.705e-06) (gnomAD).

PUS7 p.Phe101fs

Q: What condition is associated with PUS7 p.Phe101fs (c.303del)?

PUS7 p.Phe101fs (c.303del) is associated with intellectual developmental disorder with abnormal behavior, microcephaly, and short stature (ClinVar).

c.303del · rs1456834829 · VCV2431821

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (gnomAD MAF 6.705e-06)

Conditions

intellectual developmental disorder with abnormal behavior, microcephaly, and short stature

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 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 2.5, phastCons 1

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

Population frequency

dbSNP / gnomAD

Global frequency 0.00067% via dbSNP · ultra-rare

No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.

Variant & gene context

Gene: PUS7
Protein: p.Phe101fs
Coding: c.303del
MANE Select: NM_019042
dbSNP: rs1456834829
Type: Deletion
Location: chr7:105508210 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.67 · 1 PDB

Full PUS7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual developmental disorder with abnormal behavior, microcephaly, and short stature — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PUS7 p.Glu132fs Pathogenic ★★ same condition
PUS7 c.921-5del Benign ★★ same condition
PUS7 c.(1757+1_1758-1 Pathogenic ★ same condition
PUS7 p.Asn333fs Pathogenic ★ same condition
PUS7 p.Asp503fs Pathogenic ★ same condition
PUS7 p.Glu141_Ile142insTer Pathogenic ★ same condition
PUS7 p.Ile54fs Pathogenic ★ same condition
PUS7 p.Lys32fs 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/pus7-p-phe101fs (accessed [today's date]).

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