SPECC1L p.Pro80=
c.240A>G · rs201347077 · VCV2849852
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
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 -1.1 | GERP -3.5 |
| Overall | ||
| CADD | 5.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/75,066 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000494%
Overall
0.000186%
3/1,614,232 alleles · very rare
exomes 1/1,461,880 · genomes 2/152,352 · joint denominator
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
- SPECC1L
- Protein
- p.Pro80=
- Coding
- c.240A>G
- MANE Select
- NM_015330
- dbSNP
- rs201347077
- Type
- single nucleotide variant
- Location
- chr22:24313399 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.07
- Residue 80
- the 'disordered' region
Similar variants
- SPECC1L p.Pro80Leu Uncertain significance ★ ⚠ same residue
- SPECC1L p.Arg1098Gln Pathogenic/Likely pathogenic ★★ same type
- SPECC1L p.Ala1016Thr Uncertain significance ★★ ⚠ same type
- SPECC1L p.Ala180Gly Uncertain significance ★★ ⚠ same type
- SPECC1L p.Ala744Val Uncertain significance ★★ ⚠ same type
- SPECC1L p.Arg131Ter Uncertain significance ★★ same type
- SPECC1L p.Arg829Lys Uncertain significance ★★ ⚠ same type
- SPECC1L p.Glu656Ala 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/specc1l-p-pro80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown