ANKRD13D p.Pro38Ser
c.112C>T · VCV4055031
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00595%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.333 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.7, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 13 kb · p 0.00076 · regional, not allelic |
| Overall | ||
| CADD | 28.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00595%
South Asian · 5/84,060 alleles
Filtering AF
0.00234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00146%
Overall
0.00039%
6/1,537,146 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00595% | 16,812 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,034 |
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
- ANKRD13D
- Protein
- p.Pro38Ser
- Coding
- c.112C>T
- MANE Select
- NM_207354
- Type
- single nucleotide variant
- Location
- chr11:67290099 (GRCh38)
- Gene constraint
- LOEUF 0.552 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 73.38 · 1 PDB
Similar variants
- ANKRD13D p.Ala118Val Uncertain significance ★ ⚠ same type
- ANKRD13D p.Ala223Val Uncertain significance ★ ⚠ same type
- ANKRD13D p.Ala315Gly Uncertain significance ★ ⚠ same type
- ANKRD13D p.Ala441Val Uncertain significance ★ ⚠ same type
- ANKRD13D p.Ala498Gly Uncertain significance ★ same type
- ANKRD13D p.Ala536Thr Uncertain significance ★ ⚠ same type
- ANKRD13D p.Arg116His Uncertain significance ★ ⚠ same type
- ANKRD13D p.Arg146Cys 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/ankrd13d-p-pro38ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown