Is NBEA p.Val65= (c.195G>C) pathogenic?

NBEA p.Val65= (c.195G>C) is classified Likely benign in NBEA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-12-22). Absent from gnomAD v4.1; Associated with NBEA-related disorder.

What condition is associated with NBEA p.Val65= (c.195G>C)?

NBEA p.Val65= (c.195G>C) is associated with NBEA-related disorder (ClinVar).

How common is NBEA p.Val65= (c.195G>C) in the general population?

NBEA p.Val65= (c.195G>C) is absent from gnomAD v4.1 (gnomAD).

NBEA p.Val65=

c.195G>C · rs2500557830 · VCV3029096

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

NBEA-related disorder

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 2.4	GERP -0.31, phastCons 1
Overall
CADD	10.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NBEA
Protein: p.Val65=
Coding: c.195G>C
MANE Select: NM_001385012
dbSNP: rs2500557830
Type: single nucleotide variant
Location: chr13:34943015 (GRCh38)
Gene constraint: LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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

Disease context

NBEA-related disorder

Similar variants

NBEA p.Arg145Ter Pathogenic/Likely pathogenic ★★ same condition
NBEA p.Arg696Ter Pathogenic/Likely pathogenic ★★ same condition
NBEA p.Asp319Tyr Likely pathogenic ★★ same condition
NBEA p.Glu1995Lys Uncertain significance ★★ same condition
NBEA p.Gly41Ala Uncertain significance ★★ ⚠ same condition
NBEA c.2651+1G>A Likely pathogenic ★ same condition
NBEA c.2845-1G>A Likely pathogenic ★ same condition
NBEA p.Arg1302Ter 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/nbea-p-val65 (accessed [today's date]).

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