Is PUS7 p.Ser462fs (c.1385_1386del) pathogenic?

PUS7 p.Ser462fs (c.13851386del) is classified Likely pathogenic in PUS7 (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with intellectual developmental disorder with abnormal behavior, microcephaly, and short stature.

How common is PUS7 p.Ser462fs (c.1385_1386del) in the general population?

PUS7 p.Ser462fs (c.1385_1386del) is no gnomAD frequency available for this variant (gnomAD).

PUS7 p.Ser462fs

Q: What condition is associated with PUS7 p.Ser462fs (c.1385_1386del)?

PUS7 p.Ser462fs (c.1385_1386del) is associated with intellectual developmental disorder with abnormal behavior, microcephaly, and short stature (ClinVar).

c.1385_1386del · rs2133076941 · VCV1184593

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 11 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 0.92, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PUS7
Protein: p.Ser462fs
Coding: c.1385_1386del
MANE Select: NM_019042
dbSNP: rs2133076941
Type: Microsatellite
Location: chr7:105470700 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.67 · 1 PDB
Residue 462: the trud domain; a UniProt-annotated variant site (in iddabs); an α-helix

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.Leu214fs Pathogenic/Likely pathogenic ★★ same condition
PUS7 p.Leu366fs Pathogenic ★★ same condition
PUS7 p.Ser100fs Pathogenic/Likely pathogenic ★★ same condition
PUS7 c.920+4_920+7del Pathogenic ★ same condition
PUS7 c.1399-1G>C Pathogenic/Likely pathogenic ★★ same condition
PUS7 p.Asp503Tyr Pathogenic/Likely pathogenic ★★ same condition
PUS7 p.Glu132fs Pathogenic ★★ same condition
PUS7 p.Arg661His 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/pus7-p-ser462fs (accessed [today's date]).

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