Is MAP3K14 p.Phe411= (c.1233C>T) pathogenic?

MAP3K14 p.Phe411= (c.1233C>T) is classified Likely benign in MAP3K14 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-11). Ultra-rare (popmax 0.0166%, mid); Associated with NIK deficiency.

What condition is associated with MAP3K14 p.Phe411= (c.1233C>T)?

MAP3K14 p.Phe411= (c.1233C>T) is associated with NIK deficiency (ClinVar).

How common is MAP3K14 p.Phe411= (c.1233C>T) in the general population?

MAP3K14 p.Phe411= (c.1233C>T) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

How is NIK deficiency inherited?

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

MAP3K14 p.Phe411=

c.1233C>T · rs770131219 · VCV2067701

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, 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 -2.4	GERP -2.4
Overall
CADD	8.031	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0166% Middle Eastern · 1/6,022 alleles

Filtering AF 0.0089% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00706%

Overall 0.0024% 38/1,581,500 alleles · ultra-rare exomes 36/1,429,192 · genomes 2/152,308 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0166%	6,022
South Asian	0.0151%	6,624
Remaining individualsnot grpmax-eligible	0.013%	7,680
African / African-American	0.00269%	37,118
East Asian	0.00232%	43,132
Admixed American	0.00182%	55,004
European (non-Finnish)	0.00103%	96,974

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.Phe411=
Coding: c.1233C>T
MANE Select: NM_003954
dbSNP: rs770131219
Type: single nucleotide variant
Location: chr17:45284869 (GRCh38)
Gene constraint: LOEUF 0.263 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 61.00 · 8 PDB
Residue 411: the protein kinase domain; a binding site; the 'interaction with zfp91' region

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-phe411 (accessed [today's date]).

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