Is INF2 p.Arg930Gln (c.2789G>A) pathogenic?

INF2 p.Arg930Gln (c.2789G>A) is classified Conflicting classifications of pathogenicity in INF2 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-01-12). AlphaMissense: likely benign (0.1215); Very rare (popmax 0.00483%, eas); Associated with focal segmental glomerulosclerosis 5.

What condition is associated with INF2 p.Arg930Gln (c.2789G>A)?

INF2 p.Arg930Gln (c.2789G>A) is associated with focal segmental glomerulosclerosis 5, Charcot-Marie-Tooth disease dominant intermediate E (ClinVar).

How common is INF2 p.Arg930Gln (c.2789G>A) in the general population?

INF2 p.Arg930Gln (c.2789G>A) is very rare (popmax 0.00483%, eas) (gnomAD).

What do computational predictors say about INF2 p.Arg930Gln (c.2789G>A)?

AlphaMissense predicts likely benign (score 0.1215) — an in-silico prediction, not a clinical call.

INF2 p.Arg930Gln

c.2789G>A · rs752180110 · VCV1796010

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1215 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00483%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

focal segmental glomerulosclerosis 5

Computational evidence

Protein change
AlphaMissense	0.1215	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -9.31	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 6.9, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 1,931 bp · p 0.00089 · regional, not allelic
Overall
CADD	29.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00483% East Asian · 2/41,404 alleles

Filtering AF 0.00117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000995%

Overall 0.0018% 28/1,555,376 alleles · very rare exomes 26/1,403,116 · genomes 2/152,260 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00483%	20,702
African / African-American	0.00273%	36,642
South Asian	0.00235%	42,558
Admixed American	0.00195%	51,366
European (non-Finnish)	0.00183%	54,781

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: INF2
Protein: p.Arg930Gln
Coding: c.2789G>A
MANE Select: NM_022489
dbSNP: rs752180110
Type: single nucleotide variant
Location: chr14:104713220 (GRCh38)
Gene constraint: LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.34 · 10 PDB
Residue 930: an α-helix; the fh2 domain; the 'disordered' region

Full INF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

focal segmental glomerulosclerosis 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Charcot-Marie-Tooth disease dominant intermediate E

Similar variants

INF2 p.Arg930Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
INF2 p.Arg930Leu Uncertain significance ★ same residue
INF2 p.Arg930Trp Likely benign ★ ⚠ same residue
INF2 p.Arg177Cys Pathogenic/Likely pathogenic ★★ same condition
INF2 p.Arg214Cys Pathogenic/Likely pathogenic ★★ same condition
INF2 p.Arg214His Pathogenic/Likely pathogenic ★★ same condition
INF2 p.Arg218Gln Pathogenic/Likely pathogenic ★★ same condition
INF2 p.Arg218Trp Pathogenic/Likely 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/inf2-p-arg930gln (accessed [today's date]).

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