Is MAP3K20 p.Ser184fs (c.549_550del) pathogenic?

MAP3K20 p.Ser184fs (c.549550del) is classified Pathogenic in MAP3K20 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-12). No gnomAD frequency available for this variant.

How common is MAP3K20 p.Ser184fs (c.549_550del) in the general population?

MAP3K20 p.Ser184fs (c.549_550del) is no gnomAD frequency available for this variant (gnomAD).

MAP3K20 p.Ser184fs

c.549_550del · rs2468151030 · VCV2695259

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAP3K20
Protein: p.Ser184fs
Coding: c.549_550del
MANE Select: NM_016653
dbSNP: rs2468151030
Type: Microsatellite
Location: chr2:173191141 (GRCh38)
Gene constraint: LOEUF 0.569 · pLI 0.14 (gnomAD)
Structure: AlphaFold pLDDT 69.15 · 8 PDB
Residue 184: the protein kinase domain; a UniProt-annotated variant site (in cnm6; decrease of protein abundance)

Full MAP3K20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP3K20 p.Leu553del Uncertain significance ★★ same type
MAP3K20 p.Asn279del Likely pathogenic ★ same type
MAP3K20 p.Ser691del Uncertain significance ★ same type
MAP3K20 c.1552-18GTTT[2] Benign ★ same type
MAP3K20 c.350-13_350-11del Likely benign ★ same type
MAP3K20 c.987+4224GAT[7] Likely benign ★ same type
MAP3K20 c.987+4224GAT[6] Likely benign same type

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/map3k20-p-ser184fs (accessed [today's date]).

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