Is SON p.Arg10Ter (c.27dup) pathogenic?

SON p.Arg10Ter (c.27dup) is classified Pathogenic in SON (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-19). No gnomAD frequency available for this variant.

How common is SON p.Arg10Ter (c.27dup) in the general population?

SON p.Arg10Ter (c.27dup) is no gnomAD frequency available for this variant (gnomAD).

SON p.Arg10Ter

c.27dup · rs1601245742 · VCV817560

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.2	GERP 2.3, 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.Arg10Ter
Coding: c.27dup
MANE Select: NM_138927
dbSNP: rs1601245742
Type: Duplication
Location: chr21:33543114 (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

Similar variants

SON p.Arg10Ser Uncertain significance ★ ⚠ same residue
SON p.Arg1908fs Pathogenic ★★ same type
SON p.Met1025fs Likely pathogenic ★★ same type
SON p.Tyr129fs Pathogenic/Likely pathogenic ★★ same type
SON p.Arg1930_Ser1931insThrProSerArgArgSerArg Uncertain significance ★★ same type
SON p.1957SRTPSRR[7] Benign/Likely benign ★★ same type
SON p.Ala2413fs Benign ★★ same type
SON p.Ala767_Thr768insSerSerThrMetAspSerGlnMetLeuAla Likely benign ★★ same type

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-arg10ter (accessed [today's date]).

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