Is SON p.Ala1600fs (c.4799del) pathogenic?

SON p.Ala1600fs (c.4799del) is classified Pathogenic in SON (ClinVar, Single submitter, 1 submitter; last evaluated 2026-07-02). Associated with Fetal anomalies with a likely genetic cause.

What condition is associated with SON p.Ala1600fs (c.4799del)?

SON p.Ala1600fs (c.4799del) is associated with Fetal anomalies with a likely genetic cause (ClinVar).

SON p.Ala1600fs

c.4799del · VCV4887006

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Fetal anomalies with a likely genetic cause

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.7	GERP 4.4, phastCons 1

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

Variant & gene context

Gene: SON
Protein: p.Ala1600fs
Coding: c.4799del
MANE Select: NM_138927
Type: Deletion
Location: chr21:33554030 (GRCh38)
Gene constraint: LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.48 · 4 PDB

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

Disease context

Fetal anomalies with a likely genetic cause

Similar variants

SON p.Ala1653fs Likely pathogenic ★ same condition
SON p.Arg338fs Likely pathogenic ★ same condition
SON p.Gln794fs Pathogenic ★ same condition
SON p.Glu1046fs Likely pathogenic ★ same condition
SON p.Glu1449fs Likely pathogenic ★ same condition
SON p.Glu1786fs Likely pathogenic ★ same condition
SON p.Ser1306fs Pathogenic ★ same condition
SON p.Pro711fs Likely 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/son-p-ala1600fs (accessed [today's date]).

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