ENAM p.Ser1075=
c.3225C>T · rs61737041 · VCV780927
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.43%, 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 -0.14 | GERP 0.63 |
| Overall | ||
| CADD | 6.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.43%
African / African-American · 1,822/74,996 alleles
Filtering AF
2.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.3%
Overall
0.131%
2,117/1,612,990 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.43% | 41 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| Middle Eastern | 0.149% | 673 |
| Admixed American | 0.137% | 732 |
| South Asian | 0.0264% | 3,792 |
| European (non-Finnish) | 0.00729% | 13,710 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,592 |
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
- ENAM
- Protein
- p.Ser1075=
- Coding
- c.3225C>T
- MANE Select
- NM_031889
- dbSNP
- rs61737041
- Type
- single nucleotide variant
- Location
- chr4:70644651 (GRCh38)
- Gene constraint
- LOEUF 0.892 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 36.63
- Residue 1075
- the 'disordered' region
Similar variants
- ENAM c.*69T>A Uncertain significance ★★ same type
- ENAM p.Arg939Lys Uncertain significance ★★ ⚠ same type
- ENAM p.Gly631= Uncertain significance ★★ same type
- ENAM p.Ile552Met Uncertain significance ★★ ⚠ same type
- ENAM p.Leu34Pro Uncertain significance ★★ ⚠ same type
- ENAM p.Lys917Gln Uncertain significance ★★ ⚠ same type
- ENAM p.Pro1093Ser Uncertain significance ★★ ⚠ same type
- ENAM p.Thr758Pro 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/enam-p-ser1075 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown