Is NFAT5 p.Pro613= (c.1839A>G) pathogenic?

NFAT5 p.Pro613= (c.1839A>G) is classified Benign in NFAT5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-11). Rare (popmax 0.115%, afr); Associated with immunodeficiency disease.

What condition is associated with NFAT5 p.Pro613= (c.1839A>G)?

NFAT5 p.Pro613= (c.1839A>G) is associated with immunodeficiency disease (ClinVar).

How common is NFAT5 p.Pro613= (c.1839A>G) in the general population?

NFAT5 p.Pro613= (c.1839A>G) is rare (popmax 0.115%, afr) (gnomAD).

NFAT5 p.Pro613=

c.1839A>G · rs140085549 · VCV526779

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.115%, afr)

Conditions

immunodeficiency disease

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 1.9	GERP -0.8, phastCons 1
Overall
CADD	9.036	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.115% African / African-American · 86/74,896 alleles

Filtering AF 0.0952% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.088%

Overall 0.00634% 102/1,609,576 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.115%	871
Middle Eastern	0.0165%	6,052
Admixed American	0.0151%	6,604
Remaining individualsnot grpmax-eligible	0.00642%	15,584
South Asian	0.00112%	89,684
European (non-Finnish)	8.49e-05%	1,178,064

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.Pro613=
Coding: c.1839A>G
MANE Select: NM_138713
dbSNP: rs140085549
Type: single nucleotide variant
Location: chr16:69691004 (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-pro613 (accessed [today's date]).

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