Is MAP3K20 p.Asp342= (c.1026C>T) pathogenic?

MAP3K20 p.Asp342= (c.1026C>T) is classified Likely benign in MAP3K20 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-24). Ultra-rare (popmax 0.049%, eas).

How common is MAP3K20 p.Asp342= (c.1026C>T) in the general population?

MAP3K20 p.Asp342= (c.1026C>T) is ultra-rare (popmax 0.049%, eas) (gnomAD).

MAP3K20 p.Asp342=

c.1026C>T · rs80047496 · VCV3015747

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.049%, eas)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.4	GERP -5.9
Overall
CADD	7.951	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.049% East Asian · 22/44,878 alleles

Filtering AF 0.0331% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0279%

Overall 0.00192% 31/1,613,946 alleles · ultra-rare exomes 25/1,461,812 · genomes 6/152,134 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.049%	2,040
African / African-American	0.004%	24,995
South Asian	0.00329%	30,351
European (non-Finnish)	0.000254%	393,320

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: MAP3K20
Protein: p.Asp342=
Coding: c.1026C>T
MANE Select: NM_016653
dbSNP: rs80047496
Type: single nucleotide variant
Location: chr2:173229727 (GRCh38)

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

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-asp342 (accessed [today's date]).

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