Is STIL p.Ser379= (c.1137T>C) pathogenic?

STIL p.Ser379= (c.1137T>C) is classified Uncertain significance in STIL (ClinVar, Single submitter, 1 submitter; last evaluated 2013-02-08). Absent from gnomAD v4.1; Associated with microcephaly 7, primary, autosomal recessive.

What condition is associated with STIL p.Ser379= (c.1137T>C)?

STIL p.Ser379= (c.1137T>C) is associated with microcephaly 7, primary, autosomal recessive (ClinVar).

How common is STIL p.Ser379= (c.1137T>C) in the general population?

STIL p.Ser379= (c.1137T>C) is absent from gnomAD v4.1 (gnomAD).

STIL p.Ser379=

c.1137T>C · rs587784447 · VCV160050

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

microcephaly 7, primary, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP -4.7, phastCons 1
Overall
CADD	7.746	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: STIL
Protein: p.Ser379=
Coding: c.1137T>C
MANE Select: NM_001048166
dbSNP: rs587784447
Type: single nucleotide variant
Location: chr1:47282456 (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 379: the 'interaction with rbm14' region; the 'interaction with cpap' region; the 'disordered' 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.Ser379Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
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
STIL p.Arg9Gln Uncertain significance ★★ ⚠ same condition
STIL p.Asp1192Asn Uncertain significance ★★ ⚠ same condition
STIL p.Asp631Glu 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-ser379 (accessed [today's date]).

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