Is UFSP2 p.Glu93= (c.279A>G) pathogenic?

UFSP2 p.Glu93= (c.279A>G) is classified Benign/Likely benign in UFSP2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-10-24). Rare (popmax 0.846%, afr).

How common is UFSP2 p.Glu93= (c.279A>G) in the general population?

UFSP2 p.Glu93= (c.279A>G) is rare (popmax 0.846%, afr) (gnomAD).

UFSP2 p.Glu93=

c.279A>G · rs115283326 · VCV720924

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.846%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.032	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.8	GERP -2.1, phastCons 1
Overall
CADD	6.93	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.846% African / African-American · 634/74,946 alleles

Filtering AF 0.791% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.77%

Overall 0.0462% 745/1,612,274 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.846%	118
Admixed American	0.0852%	1,174
Remaining individualsnot grpmax-eligible	0.0801%	1,249
Middle Eastern	0.0165%	6,048
South Asian	0.00661%	15,124
European (non-Finnish)	0.000254%	393,035

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: UFSP2
Protein: p.Glu93=
Coding: c.279A>G
MANE Select: NM_001114357 · reported on NM_018359
dbSNP: rs115283326
Type: single nucleotide variant
Location: chr4:185418495 (GRCh38)

Full UFSP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/ufsp2-p-glu93 (accessed [today's date]).

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