HCCS p.Ala7=
c.21T>C · rs752860604 · VCV2045948
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00146%, 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 0.37 | GERP -1, phastCons 0.47 |
| Overall | ||
| CADD | 8.981 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00146%
European (non-Finnish) · 13/892,503 alleles
Filtering AF
0.000813%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000626%
Overall
0.00108%
13/1,207,681 alleles · very rare
exomes 12/1,094,991 · genomes 1/112,690 · 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
- HCCS
- Protein
- p.Ala7=
- Coding
- c.21T>C
- MANE Select
- NM_005333
- dbSNP
- rs752860604
- Type
- single nucleotide variant
- Location
- chrX:11112081 (GRCh38)
- Structure
- AlphaFold pLDDT 78.84
- Residue 7
- the 'disordered' region
Similar variants
- HCCS p.Arg217Cys Likely pathogenic ★★ same type
- HCCS p.Trp135Ter Likely pathogenic ★★ same type
- HCCS p.Ala19Pro Uncertain significance ★★ ⚠ same type
- HCCS p.Ala60Thr Uncertain significance ★★ ⚠ same type
- HCCS c.101-11G>C Benign/Likely benign ★★ same type
- HCCS c.402-331A>G Benign ★★ same type
- HCCS p.Ala17Ser Likely benign ★★ same type
- HCCS p.Ala262Gly Benign/Likely 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/hccs-p-ala7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown