Is NEBL p.Pro578= (c.1734T>C) pathogenic?

NEBL p.Pro578= (c.1734T>C) is classified Benign in NEBL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-30). No allele count reported in gnomAD v4.1 (AN 1,597,318).

How common is NEBL p.Pro578= (c.1734T>C) in the general population?

NEBL p.Pro578= (c.1734T>C) is no allele count reported in gnomAD v4.1 (AN 1,597,318) (gnomAD).

NEBL p.Pro578=

c.1734T>C · rs2491742102 · VCV3234014

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,597,318)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.024	GERP -3, phastCons 0.049
Overall
CADD	6.507	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,597,318). 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: NEBL
Protein: p.Pro578=
Coding: c.1734T>C
MANE Select: NM_006393
dbSNP: rs2491742102
Type: single nucleotide variant
Location: chr10:20828572 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 62.00 · 1 PDB

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

Similar variants

NEBL p.Pro578Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
NEBL c.1227+5G>A Uncertain significance ★★ same type
NEBL c.1870-1G>A Uncertain significance ★★ same type
NEBL c.798+1G>A Uncertain significance ★★ same type
NEBL c.903+1G>T Uncertain significance ★★ same type
NEBL p.Ala114Ser Uncertain significance ★★ ⚠ same type
NEBL p.Ala209Ser Uncertain significance ★★ ⚠ same type
NEBL p.Ala219Thr Uncertain significance ★★ ⚠ 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/nebl-p-pro578 (accessed [today's date]).

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