Is ERF p.Ser295fs (c.879del) pathogenic?

ERF p.Ser295fs (c.879del) is classified Likely pathogenic in ERF (ClinVar, Single submitter, 1 submitter; last evaluated 2017-07-19). Absent from gnomAD v4.1.

How common is ERF p.Ser295fs (c.879del) in the general population?

ERF p.Ser295fs (c.879del) is absent from gnomAD v4.1 (gnomAD).

ERF p.Ser295fs

c.879del · rs1555750642 · VCV445429

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,926)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.6	GERP 1.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,926). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ERF
Protein: p.Ser295fs
Coding: c.879del
MANE Select: NM_006494
dbSNP: rs1555750642
Type: Deletion
Location: chr19:42249233 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 55.46 · 2 PDB
Residue 295: the 'disordered' region

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

Similar variants

ERF p.Ser295= Likely benign ★★ same residue
ERF p.Arg143fs Pathogenic/Likely pathogenic ★★ same type
ERF p.Asp188_Cys189insTer Pathogenic ★★ same type
ERF p.Gly299fs Pathogenic/Likely pathogenic ★★ same type
ERF p.Lys401fs Pathogenic/Likely pathogenic ★★ same type
ERF p.Pro133fs Likely pathogenic ★★ same type
ERF p.Pro358fs Pathogenic/Likely pathogenic ★★ same type
ERF p.Ser304del Pathogenic ★★ same type

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/erf-p-ser295fs (accessed [today's date]).

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