Is NEBL p.Ser901= (c.2703C>T) pathogenic?

NEBL p.Ser901= (c.2703C>T) is classified Likely benign in NEBL (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-21). Very rare (popmax 0.00678%, nfe); Associated with dilated cardiomyopathy.

What condition is associated with NEBL p.Ser901= (c.2703C>T)?

NEBL p.Ser901= (c.2703C>T) is associated with dilated cardiomyopathy (ClinVar).

How common is NEBL p.Ser901= (c.2703C>T) in the general population?

NEBL p.Ser901= (c.2703C>T) is very rare (popmax 0.00678%, nfe) (gnomAD).

NEBL p.Ser901=

c.2703C>T · rs374451899 · VCV1088033

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00678%, nfe)

Conditions

dilated cardiomyopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -15	GERP -5.2
Overall
CADD	0.219	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00678% European (non-Finnish) · 80/1,179,896 alleles

Filtering AF 0.00555% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.00552% 89/1,613,766 alleles · very rare exomes 83/1,461,692 · genomes 6/152,074 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00678%	14,749
African / African-American	0.00534%	18,718
Remaining individualsnot grpmax-eligible	0.0048%	20,827
Admixed American	0.00167%	59,980
South Asian	0.0011%	91,076

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: NEBL
Protein: p.Ser901=
Coding: c.2703C>T
MANE Select: NM_006393
dbSNP: rs374451899
Type: single nucleotide variant
Location: chr10:20808568 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 62.00 · 1 PDB
Residue 901: the 'linker' region

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

Disease context

dilated cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NEBL c.1227+5G>A Uncertain significance ★★ same condition
NEBL c.1870-1G>A Uncertain significance ★★ same condition
NEBL c.798+1G>A Uncertain significance ★★ same condition
NEBL c.903+1G>T Uncertain significance ★★ same condition
NEBL p.Ala114Ser Uncertain significance ★★ ⚠ same condition
NEBL p.Ala219Thr Uncertain significance ★★ ⚠ same condition
NEBL p.Ala264Val Uncertain significance ★★ ⚠ same condition
NEBL p.Ala440Asp Uncertain significance ★★ ⚠ 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/nebl-p-ser901 (accessed [today's date]).

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