Is INF2 p.Ser293= (c.879G>A) pathogenic?

INF2 p.Ser293= (c.879G>A) is classified Conflicting classifications of pathogenicity in INF2 (ClinVar, Conflicting submitters, 14 submitters; last evaluated 2026-02-02). Low-frequency (popmax 2.14%, amr); Associated with focal segmental glomerulosclerosis 5.

What condition is associated with INF2 p.Ser293= (c.879G>A)?

INF2 p.Ser293= (c.879G>A) is associated with focal segmental glomerulosclerosis 5, kidney disorder, Charcot-Marie-Tooth disease dominant intermediate E (ClinVar).

How common is INF2 p.Ser293= (c.879G>A) in the general population?

INF2 p.Ser293= (c.879G>A) is low-frequency (popmax 2.14%, amr) (gnomAD).

INF2 p.Ser293=

c.879G>A · rs184709736 · VCV261629

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 14 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.14%, amr)

Conditions

focal segmental glomerulosclerosis 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.60 · evaluated, not missing
Constraint at this position
Conservation	phyloP -20	GERP -14
Overall
CADD	0.046	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.14% Admixed American · 1,283/59,898 alleles

Filtering AF 2.04% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.01%

Overall 0.689% 11,053/1,603,198 alleles · low-frequency exomes 10,244/1,451,016 · genomes 809/152,182 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	2.14%	47
European (non-Finnish)	0.726%	138
Remaining individualsnot grpmax-eligible	0.698%	143
Middle Eastern	0.671%	149
Ashkenazi Jewishnot grpmax-eligible	0.414%	242
South Asian	0.396%	253
African / African-American	0.197%	506
Finnishnot grpmax-eligible	0.196%	510
East Asian	0.00446%	22,424

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.Ser293=
Coding: c.879G>A
MANE Select: NM_022489
dbSNP: rs184709736
Type: single nucleotide variant
Location: chr14:104706945 (GRCh38)
Gene constraint: LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.34 · 10 PDB
Residue 293: the gbd/fh3 domain

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: kidney disorder Charcot-Marie-Tooth disease dominant intermediate E

Similar variants

INF2 p.Ser293Leu Uncertain significance ★★ ⚠ 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
INF2 p.Arg91Gly Pathogenic/Likely pathogenic ★★ same condition
INF2 p.Asn202Asp 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-ser293 (accessed [today's date]).

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