CCDC112 p.Leu401=
c.1203A>G · rs202145172 · VCV739607
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.17%, sas)
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 -3 | GERP -2.5 |
| Overall | ||
| CADD | 2.749 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.17%
South Asian · 1,058/90,590 alleles
Filtering AF
1.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.0865%
1,396/1,612,992 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.17% | 86 |
| Middle Eastern | 0.396% | 252 |
| Remaining individualsnot grpmax-eligible | 0.0912% | 1,096 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,466 |
| European (non-Finnish) | 0.0198% | 5,042 |
| Admixed American | 0.01% | 9,977 |
| African / African-American | 0.00667% | 15,002 |
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
- CCDC112
- Protein
- p.Leu401=
- Coding
- c.1203A>G
- MANE Select
- NM_001040440
- dbSNP
- rs202145172
- Type
- single nucleotide variant
- Location
- chr5:115271342 (GRCh38)
- Gene constraint
- LOEUF 0.875 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.18
- Residue 401
- the 'disordered' region
Similar variants
- CCDC112 p.Ala165Val Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala299Ser Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala434Pro Uncertain significance ★ ⚠ same type
- CCDC112 p.Ala68Pro Uncertain significance ★ same type
- CCDC112 p.Arg391Cys Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg391His Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg391Leu Uncertain significance ★ ⚠ same type
- CCDC112 p.Arg393Leu 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/ccdc112-p-leu401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown