Is NFAT5 p.Gly485= (c.1455C>G) pathogenic?

NFAT5 p.Gly485= (c.1455C>G) is classified Likely benign in NFAT5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-12). Very rare (popmax 0.000339%, nfe); Associated with immunodeficiency disease.

What condition is associated with NFAT5 p.Gly485= (c.1455C>G)?

NFAT5 p.Gly485= (c.1455C>G) is associated with immunodeficiency disease (ClinVar).

How common is NFAT5 p.Gly485= (c.1455C>G) in the general population?

NFAT5 p.Gly485= (c.1455C>G) is very rare (popmax 0.000339%, nfe) (gnomAD).

NFAT5 p.Gly485=

c.1455C>G · rs2544088907 · VCV2169334

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Conditions

immunodeficiency disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.83 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3.6	GERP 1.5, phastCons 1
Overall
CADD	10.62	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,179,672 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,460,714 alleles · very rare

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: NFAT5
Protein: p.Gly485=
Coding: c.1455C>G
MANE Select: NM_138713
dbSNP: rs2544088907
Type: single nucleotide variant
Location: chr16:69670062 (GRCh38)
Gene constraint: LOEUF 0.235 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 44.83 · 1 PDB

Full NFAT5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

NFAT5 p.Ala1219Ser Uncertain significance ★★ ⚠ same condition
NFAT5 p.Ala632Val Uncertain significance ★★ ⚠ same condition
NFAT5 p.Ala712Val Uncertain significance ★★ ⚠ same condition
NFAT5 p.Arg220Gln Uncertain significance ★★ ⚠ same condition
NFAT5 p.Arg582Lys Uncertain significance ★★ ⚠ same condition
NFAT5 p.Arg737Gly Uncertain significance ★★ ⚠ same condition
NFAT5 p.Asn1053Ser Uncertain significance ★★ ⚠ same condition
NFAT5 p.Asn1306Ser 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/nfat5-p-gly485 (accessed [today's date]).

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