Is SCRIB p.Glu679del (c.2025GGA[3]) pathogenic?

SCRIB p.Glu679del (c.2025GGA[3]) is classified Likely benign in SCRIB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-08-02). Rare (popmax 0.366%, afr); Associated with SCRIB-related disorder.

What condition is associated with SCRIB p.Glu679del (c.2025GGA[3])?

SCRIB p.Glu679del (c.2025GGA[3]) is associated with SCRIB-related disorder (ClinVar).

How common is SCRIB p.Glu679del (c.2025GGA[3]) in the general population?

SCRIB p.Glu679del (c.2025GGA[3]) is rare (popmax 0.366%, afr) (gnomAD).

SCRIB p.Glu679del

c.2025GGA[3] · rs761421987 · VCV3036010

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.366%, afr)

Conditions

SCRIB-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4.8	GERP -1.6
Overall
CADD	3.069	PHRED · no single calibrated threshold — expert panels disagree
Region caveats
Repeat context	tandem	(CCT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.366% African / African-American · 266/72,698 alleles

Filtering AF 0.33% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.316%

Overall 0.0199% 308/1,544,972 alleles · rare exomes 161/1,392,806 · genomes 147/152,166 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.366%	273
Remaining individualsnot grpmax-eligible	0.0185%	5,414
Admixed American	0.0161%	6,200
Ashkenazi Jewishnot grpmax-eligible	0.00408%	24,530
South Asian	0.00255%	39,182
European (non-Finnish)	0.00174%	57,400

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SCRIB
Protein: p.Glu679del
Coding: c.2025GGA[3]
MANE Select: NM_182706
dbSNP: rs761421987
Type: Microsatellite
Location: chr8:143808688 (GRCh38)
Gene constraint: LOEUF 0.684 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.33 · 42 PDB
Residue 679: the 'sufficient for targeting to adherens junction and to inhibit cell proliferation' region; the 'disordered' region

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

Disease context

SCRIB-related disorder

Similar variants

SCRIB c.3715-19TGCTC[4] Likely benign same condition
SCRIB p.Ala796fs Uncertain significance ★ same condition
SCRIB p.Arg231Gln Uncertain significance ★ ⚠ same condition
SCRIB c.2179-10C>T Likely benign same condition
SCRIB c.3714+7G>A Likely benign same condition
SCRIB c.3910-3dup Likely benign same condition
SCRIB c.4018-6C>T Likely benign same condition
SCRIB c.4514+8C>T Likely benign 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/scrib-p-glu679del (accessed [today's date]).

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