Is NBAS p.Val596Met (c.1786G>A) pathogenic?

NBAS p.Val596Met (c.1786G>A) is classified Uncertain significance in NBAS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-04-01). AlphaMissense: likely benign (0.1534); Rare (popmax 0.214%, mid); Associated with Inborn genetic diseases.

What condition is associated with NBAS p.Val596Met (c.1786G>A)?

NBAS p.Val596Met (c.1786G>A) is associated with Inborn genetic diseases (ClinVar).

How common is NBAS p.Val596Met (c.1786G>A) in the general population?

NBAS p.Val596Met (c.1786G>A) is rare (popmax 0.214%, mid) (gnomAD).

What do computational predictors say about NBAS p.Val596Met (c.1786G>A)?

AlphaMissense predicts likely benign (score 0.1534) — an in-silico prediction, not a clinical call.

NBAS p.Val596Met

c.1786G>A · rs920633717 · VCV1199778

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1534 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.214%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1534	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -8.23	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 0.98, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 394 kb · p 0.09 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.214% Middle Eastern · 13/6,084 alleles

Filtering AF 0.126% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.1%

Overall 0.0013% 21/1,613,958 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.214%	468
Remaining individualsnot grpmax-eligible	0.0048%	20,827
African / African-American	0.00133%	74,930
South Asian	0.0011%	91,086
European (non-Finnish)	0.000254%	393,321

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: NBAS
Protein: p.Val596Met
Coding: c.1786G>A
MANE Select: NM_015909
dbSNP: rs920633717
Type: single nucleotide variant
Location: chr2:15468473 (GRCh38)
Gene constraint: LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 74.42
Residue 596: a UniProt-annotated variant site (in ilfs2; uncertain significance); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance); the 'interaction with use1' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NBAS p.Val596Ala Uncertain significance ★ ⚠ same residue
NBAS p.Ala1568Val Uncertain significance ★★ ⚠ same condition
NBAS p.Ala1645Val Uncertain significance ★★ ⚠ same condition
NBAS p.Ala1795Val Uncertain significance ★★ ⚠ same condition
NBAS p.Ala1941Gly Uncertain significance ★★ ⚠ same condition
NBAS p.Ala195Thr Uncertain significance ★★ ⚠ same condition
NBAS p.Ala2005Thr Uncertain significance ★★ ⚠ same condition
NBAS p.Ala2341Val 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/nbas-p-val596met (accessed [today's date]).

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