Is STIL p.Asp830fs (c.2488_2489del) pathogenic?

STIL p.Asp830fs (c.24882489del) is classified Likely pathogenic in STIL (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-01). Absent from gnomAD; Associated with microcephaly 7, primary, autosomal recessive.

What condition is associated with STIL p.Asp830fs (c.2488_2489del)?

STIL p.Asp830fs (c.2488_2489del) is associated with microcephaly 7, primary, autosomal recessive (ClinVar).

How common is STIL p.Asp830fs (c.2488_2489del) in the general population?

STIL p.Asp830fs (c.2488_2489del) is absent from gnomAD (gnomAD).

STIL p.Asp830fs

c.2488_2489del · rs2523341350 · VCV1705699

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

microcephaly 7, primary, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 14 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.74	GERP -0.13, phastCons 0.95

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: STIL
Protein: p.Asp830fs
Coding: c.2488_2489del
MANE Select: NM_001048166
dbSNP: rs2523341350
Type: Deletion
Location: chr1:47269761 (GRCh38)
Gene constraint: LOEUF 0.575 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 54.29 · 5 PDB
Residue 830: the 'interaction with rbm14' region

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

Disease context

microcephaly 7, primary, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

STIL p.Asp830Ala Uncertain significance ★ ⚠ same residue
STIL p.Pro23fs Uncertain significance ★ same condition
STIL p.Leu1219_Val1220insTer Pathogenic same condition
STIL p.Leu782fs Likely pathogenic same condition
STIL c.*203C>T Uncertain significance ★★ same condition
STIL c.*599A>G Uncertain significance ★★ same condition
STIL p.Ala543Val Uncertain significance ★★ ⚠ same condition
STIL p.Arg742His Uncertain significance ★★ ⚠ 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/stil-p-asp830fs (accessed [today's date]).

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