ARNT2 p.Ser343=
c.1029C>T · rs139389870 · VCV1664669
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.412%, afr)
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 -10 | GERP -3.7 |
| Overall | ||
| CADD | 0.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.412%
African / African-American · 309/75,046 alleles
Filtering AF
0.374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.359%
Overall
0.023%
372/1,614,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.412% | 243 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,473 |
| Admixed American | 0.025% | 4,001 |
| Middle Eastern | 0.0165% | 6,062 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.00229% | 43,702 |
| South Asian | 0.0011% | 91,056 |
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
- ARNT2
- Protein
- p.Ser343=
- Coding
- c.1029C>T
- MANE Select
- NM_014862
- dbSNP
- rs139389870
- Type
- single nucleotide variant
- Location
- chr15:80552714 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 59.49
- Residue 343
- the pas 2 domain
Similar variants
- ARNT2 p.Ser343Pro Uncertain significance ★★ ⚠ same residue
- ARNT2 p.Arg159Ter Pathogenic/Likely pathogenic ★★ same type
- ARNT2 p.Ala483Val Uncertain significance ★★ ⚠ same type
- ARNT2 p.Arg262Lys Uncertain significance ★★ ⚠ same type
- ARNT2 p.Asp705Tyr Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gln520Arg Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gly472Ser Uncertain significance ★★ ⚠ same type
- ARNT2 p.Gly546Arg 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/arnt2-p-ser343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown