Is JARID2 p.Pro402= (c.1206C>T) pathogenic?

JARID2 p.Pro402= (c.1206C>T) is classified Benign in JARID2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-18). Common (popmax 34.1%, mid) — too common for a highly-penetrant pathogenic allele.

JARID2 p.Pro402=

Q: How common is JARID2 p.Pro402= (c.1206C>T) in the general population?

JARID2 p.Pro402= (c.1206C>T) is common (popmax 34.1%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1206C>T · rs742099 · VCV1272172

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 34.1%, mid) — too common for a highly-penetrant pathogenic allele

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 -1.7	GERP -1.3
Overall
CADD	9.736	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 34.1% Middle Eastern · 2,068/6,062 alleles

Filtering AF 32.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 32.4%

Overall 23.8% 383,332/1,613,708 alleles · common exomes 352,216/1,461,578 · genomes 31,116/152,130 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	34.1%	3
Ashkenazi Jewishnot grpmax-eligible	30.2%	3
East Asian	26.2%	4
Remaining individualsnot grpmax-eligible	25%	4
European (non-Finnish)	24.8%	4
Finnishnot grpmax-eligible	24.7%	4
Amishnot grpmax-eligible	23.5%	4
Admixed American	21.5%	5
South Asian	19.1%	5
African / African-American	7.86%	13

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: JARID2
Protein: p.Pro402=
Coding: c.1206C>T
MANE Select: NM_004973
dbSNP: rs742099
Type: single nucleotide variant
Location: chr6:15496431 (GRCh38)
Gene constraint: LOEUF 0.202 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 62.74 · 17 PDB
Residue 402: the 'disordered' region

Full JARID2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

JARID2 p.Pro402His Uncertain significance ★ ⚠ same residue
JARID2 p.Ala265Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Ala844Pro Uncertain significance ★★ ⚠ same type
JARID2 p.Arg311Gly Uncertain significance ★★ ⚠ same type
JARID2 p.Asn1155Tyr Uncertain significance ★★ ⚠ same type
JARID2 p.Asn171Asp Uncertain significance ★★ ⚠ same type
JARID2 p.Asn383Ser Uncertain significance ★★ ⚠ same type
JARID2 p.Glu186Gln Uncertain significance ★★ ⚠ 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/jarid2-p-pro402 (accessed [today's date]).

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