Is SIN3A p.Ser587fs (c.1759del) pathogenic?

SIN3A p.Ser587fs (c.1759del) is classified Pathogenic in SIN3A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2016-08-12). Absent from gnomAD; Associated with SIN3A-related intellectual disability syndrome due to a point mutation.

What condition is associated with SIN3A p.Ser587fs (c.1759del)?

SIN3A p.Ser587fs (c.1759del) is associated with SIN3A-related intellectual disability syndrome due to a point mutation (ClinVar).

How common is SIN3A p.Ser587fs (c.1759del) in the general population?

SIN3A p.Ser587fs (c.1759del) is absent from gnomAD (gnomAD).

SIN3A p.Ser587fs

c.1759del · rs879255620 · VCV253072

Pathogenic No assertion criteria

Classification

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

SIN3A-related intellectual disability syndrome due to a point mutation

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 12 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 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: SIN3A
Protein: p.Ser587fs
Coding: c.1759del
MANE Select: NM_001145358
dbSNP: rs879255620
Type: Deletion
Location: chr15:75400135 (GRCh38)
Gene constraint: LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 69.67
Residue 587: the 'interaction with ncor1' region; the 'interaction with suds3 and sap130' region

Full SIN3A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SIN3A-related intellectual disability syndrome due to a point mutation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SIN3A p.Lys937fs Pathogenic ★★ same condition
SIN3A p.Lys948fs Pathogenic/Likely pathogenic ★★ same condition
SIN3A p.Arg340fs Pathogenic ★ same condition
SIN3A p.His731fs Pathogenic ★ same condition
SIN3A p.Lys410fs Pathogenic ★ same condition
SIN3A p.Ser600fs Likely pathogenic ★ same condition
SIN3A p.Tyr1262fs Likely pathogenic ★ same condition
SIN3A p.Val58fs 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/sin3a-p-ser587fs (accessed [today's date]).

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