SPEF2 p.Pro666=
c.1998A>G · VCV4969853
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.04%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP 0.64 |
| Overall | ||
| CADD | 1.841 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.04%
African / African-American · 782/74,916 alleles
Filtering AF
0.983%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.959%
Overall
0.053%
853/1,610,810 alleles · low-frequency
exomes 370/1,458,462 · genomes 483/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.04% | 96 |
| Admixed American | 0.0554% | 1,806 |
| Remaining individualsnot grpmax-eligible | 0.0497% | 2,011 |
| Middle Eastern | 0.0165% | 6,050 |
| South Asian | 0.00111% | 90,284 |
| European (non-Finnish) | 0.000424% | 235,711 |
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
- SPEF2
- Protein
- p.Pro666=
- Coding
- c.1998A>G
- MANE Select
- NM_024867
- Type
- single nucleotide variant
- Location
- chr5:35695757 (GRCh38)
- Gene constraint
- LOEUF 0.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.30
- Residue 666
- a UniProt-annotated variant site (in spgf43; loss of protein expression; changed sperm axoneme assembly); a UniProt-annotated variant site (found in a female patient with primary ciliary dyskinesia-like symptoms including chronic sinusitis, bronchitis, chronic wet cough and recurrent pneumonia; uncertain significance)
Similar variants
- SPEF2 p.Asp797Gly Uncertain significance ★★ ⚠ same type
- SPEF2 p.Glu116Lys Uncertain significance ★★ ⚠ same type
- SPEF2 p.Glu1752Gln Uncertain significance ★★ ⚠ same type
- SPEF2 c.1167+46T>C Benign ★★ same type
- SPEF2 c.1168-85A>G Benign ★★ same type
- SPEF2 c.1525-111C>G Benign ★★ same type
- SPEF2 c.2037+17A>C Benign ★★ same type
- SPEF2 c.2141+130C>T Benign ★★ 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/spef2-p-pro666 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown