Is MAP3K14 p.Arg366= (c.1098A>G) pathogenic?

MAP3K14 p.Arg366= (c.1098A>G) is classified Likely benign in MAP3K14 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-01). Ultra-rare (popmax 0.0494%, mid); Associated with NIK deficiency.

What condition is associated with MAP3K14 p.Arg366= (c.1098A>G)?

MAP3K14 p.Arg366= (c.1098A>G) is associated with NIK deficiency (ClinVar).

How common is MAP3K14 p.Arg366= (c.1098A>G) in the general population?

MAP3K14 p.Arg366= (c.1098A>G) is ultra-rare (popmax 0.0494%, mid) (gnomAD).

How is NIK deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

MAP3K14 p.Arg366=

c.1098A>G · rs772065458 · VCV844949

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0494%, mid)

Conditions

NIK deficiency

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 0.76	GERP -2.1, phastCons 1
Overall
CADD	5.525	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0494% Middle Eastern · 3/6,068 alleles

Filtering AF 0.0134% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00717%

Overall 0.00131% 21/1,604,148 alleles · ultra-rare exomes 19/1,451,966 · genomes 2/152,182 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0494%	2,023
South Asian	0.00447%	22,360
Ashkenazi Jewishnot grpmax-eligible	0.00342%	29,252
Remaining individualsnot grpmax-eligible	0.00322%	31,053
European (non-Finnish)	0.000936%	106,825

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: MAP3K14
Protein: p.Arg366=
Coding: c.1098A>G
MANE Select: NM_003954
dbSNP: rs772065458
Type: single nucleotide variant
Location: chr17:45286485 (GRCh38)
Gene constraint: LOEUF 0.263 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 61.00 · 8 PDB

Full MAP3K14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For NIK deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

MAP3K14 p.Ala103Thr Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Ala142Ser Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Ala575Thr Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Arg131His Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Arg146Gln Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Arg218Gln Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Arg432Trp Uncertain significance ★★ ⚠ same condition
MAP3K14 p.Arg99His 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/map3k14-p-arg366 (accessed [today's date]).

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