MCCC2 c.196+113del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 21.9%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| Splice region | donor +113 | deep intronic (+113 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Non-coding constraint | Z -0.51 | 1 kb window · o/e 1.04 · regional · uncalibrated |
| Overall | ||
| CADD | 0.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.9%
South Asian · 10,470/47,702 alleles
Filtering AF
21.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 21.5%
Overall
14.5%
106,651/737,620 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 21.9% | 5 |
| Remaining individualsnot grpmax-eligible | 17.3% | 6 |
| Finnishnot grpmax-eligible | 16.9% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 14.8% | 7 |
| Middle Eastern | 14.7% | 7 |
| European (non-Finnish) | 14.5% | 7 |
| East Asian | 12.9% | 8 |
| Admixed American | 9.14% | 11 |
| African / African-American | 7.72% | 13 |
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
- MCCC2
- Coding
- c.196+113del
- MANE Select
- NM_022132
- dbSNP
- rs72536613
- Type
- Deletion
- Location
- chr5:71593090 (GRCh38)
- Gene constraint
- LOEUF 0.832 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.82 · 14 PDB
Similar variants
- MCCC2 c.1151del Likely pathogenic ★★ same type
- MCCC2 c.281+1del Likely pathogenic ★★ same type
- MCCC2 c.383+2del Likely pathogenic ★★ same type
- MCCC2 c.739del Pathogenic/Likely pathogenic ★★ same type
- MCCC2 p.Asn230fs Pathogenic/Likely pathogenic ★★ same type
- MCCC2 p.Gly118del Pathogenic/Likely pathogenic ★★ same type
- MCCC2 p.Gly368fs Pathogenic/Likely pathogenic ★★ same type
- MCCC2 p.Gly79fs Pathogenic/Likely pathogenic ★★ 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/mccc2-c-196-plus-113del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown