CCDC116 p.Leu313=
c.937C>T · rs141095413 · VCV2652946
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.495%, mid)
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 0.8 | GERP 0.65, phastCons 0.39 |
| Overall | ||
| CADD | 2.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.495%
Middle Eastern · 30/6,062 alleles
Filtering AF
0.356%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.309%
Overall
0.0592%
954/1,611,314 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.495% | 202 |
| Admixed American | 0.113% | 883 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| European (non-Finnish) | 0.065% | 1,538 |
| South Asian | 0.0253% | 3,960 |
| African / African-American | 0.0213% | 4,691 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,882 |
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
- CCDC116
- Protein
- p.Leu313=
- Coding
- c.937C>T
- MANE Select
- NM_152612
- dbSNP
- rs141095413
- Type
- single nucleotide variant
- Location
- chr22:21635000 (GRCh38)
- Gene constraint
- LOEUF 1.158 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59
Similar variants
- CCDC116 c.73-8C>T Benign ★★ same type
- CCDC116 p.Arg174= Benign ★★ same type
- CCDC116 p.Asn302= Benign ★★ same type
- CCDC116 p.Lys412Arg Benign ★★ same type
- CCDC116 p.Pro293Leu Benign ★★ same type
- CCDC116 p.Thr569= Benign ★★ same type
- CCDC116 p.Val252Met Benign ★★ same type
- CCDC116 p.Ala12Asp 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/ccdc116-p-leu313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown