Is SON p.Arg1850fs (c.5549_5550del) pathogenic?

SON p.Arg1850fs (c.55495550del) is classified Pathogenic in SON (ClinVar, Single submitter, 3 submitters; last evaluated 2014-07-14). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with SON p.Arg1850fs (c.5549_5550del)?

SON p.Arg1850fs (c.5549_5550del) is associated with Inborn genetic diseases, ZTTK syndrome (ClinVar).

How common is SON p.Arg1850fs (c.5549_5550del) in the general population?

SON p.Arg1850fs (c.5549_5550del) is no gnomAD frequency available for this variant (gnomAD).

SON p.Arg1850fs

c.5549_5550del · rs886039774 · VCV265774

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 11	GERP 4.2, 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: SON
Protein: p.Arg1850fs
Coding: c.5549_5550del
MANE Select: NM_138927
dbSNP: rs886039774
Type: Microsatellite
Location: chr21:33554777 (GRCh38)
Gene constraint: LOEUF 0.051 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.48 · 4 PDB
Residue 1850: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ZTTK syndrome

Similar variants

SON p.Gln874fs Pathogenic ★★ same condition
SON p.Leu1593fs Pathogenic ★★ same condition
SON p.1036AYERSMMS[1] Likely benign ★★ same condition
SON p.Arg1998_Arg1999insSerArgThrProSerArgArg Likely benign ★★ same condition
SON p.Asp1819fs Likely pathogenic ★ same condition
SON p.Glu1206fs Pathogenic ★ same condition
SON p.Arg1884del Uncertain significance ★ same condition
SON p.Asp1627del Conflicting classifications of pathogenicity ★ 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-arg1850fs (accessed [today's date]).

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