Is SP9 p.Arg403fs (c.1192_1207dup) pathogenic?

SP9 p.Arg403fs (c.11921207dup) is classified Pathogenic in SP9 (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with intellectual disability.

What condition is associated with SP9 p.Arg403fs (c.1192_1207dup)?

SP9 p.Arg403fs (c.1192_1207dup) is associated with intellectual disability (ClinVar).

How common is SP9 p.Arg403fs (c.1192_1207dup) in the general population?

SP9 p.Arg403fs (c.1192_1207dup) is no gnomAD frequency available for this variant (gnomAD).

SP9 p.Arg403fs

c.1192_1207dup · rs2105510265 · VCV1297469

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

intellectual disability

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -5.5, 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: SP9
Protein: p.Arg403fs
Coding: c.1192_1207dup
MANE Select: NM_001145250
dbSNP: rs2105510265
Type: Duplication
Location: chr2:174337273 (GRCh38)
Gene constraint: LOEUF 0.731 · pLI 0.58 (gnomAD)
Structure: AlphaFold pLDDT 49.04

Full SP9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SP9 p.Glu378Gly Pathogenic ★ same condition
SP9 p.Glu378Ala Likely pathogenic same condition
SP9 p.His406fs 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/sp9-p-arg403fs (accessed [today's date]).

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