CCDC62 p.Ile14=
c.42C>T · rs61956960 · VCV2643506
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.47%, nfe)
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 -0.57 | GERP -3.9, phastCons 0.014 |
| Overall | ||
| CADD | 6.679 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.47%
European (non-Finnish) · 17,227/1,175,252 alleles
Filtering AF
1.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.44%
Overall
1.2%
19,197/1,606,116 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.47% | 68 |
| Remaining individualsnot grpmax-eligible | 1.01% | 99 |
| Middle Eastern | 0.894% | 112 |
| Ashkenazi Jewishnot grpmax-eligible | 0.791% | 126 |
| Finnishnot grpmax-eligible | 0.593% | 169 |
| Admixed American | 0.555% | 180 |
| African / African-American | 0.211% | 473 |
| South Asian | 0.206% | 486 |
| East Asian | 0.00671% | 14,909 |
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
- CCDC62
- Protein
- p.Ile14=
- Coding
- c.42C>T
- MANE Select
- NM_201435
- dbSNP
- rs61956960
- Type
- single nucleotide variant
- Location
- chr12:122777496 (GRCh38)
- Gene constraint
- LOEUF 1.012 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.07
Similar variants
- CCDC62 p.Gln364= Benign ★★ same type
- CCDC62 p.Ala190Gly Uncertain significance ★ ⚠ same type
- CCDC62 p.Ala271Glu Uncertain significance ★ ⚠ same type
- CCDC62 p.Ala271Ser Uncertain significance ★ ⚠ same type
- CCDC62 p.Ala322Asp Uncertain significance ★ ⚠ same type
- CCDC62 p.Ala503Gly Uncertain significance ★ ⚠ same type
- CCDC62 p.Ala6Ser Uncertain significance ★ ⚠ same type
- CCDC62 p.Arg11Cys 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/ccdc62-p-ile14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown