HCCS p.Ala55fs
c.163del · VCV4291739
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
linear skin defects with multiple congenital anomalies 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3.2, phastCons 0.004 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- HCCS
- Protein
- p.Ala55fs
- Coding
- c.163del
- MANE Select
- NM_005333
- Type
- Deletion
- Location
- chrX:11114897 (GRCh38)
- Structure
- AlphaFold pLDDT 78.84
Similar variants
- HCCS p.Arg217Cys Likely pathogenic ★★ same condition
- HCCS p.Trp135Ter Likely pathogenic ★★ same condition
- HCCS p.Glu233Lys Benign/Likely benign ★★ same condition
- HCCS p.Arg217His Likely pathogenic ★ same condition
- HCCS p.Gln239Ter Likely pathogenic ★ same condition
- HCCS p.Met1Thr Likely pathogenic ★ same condition
- HCCS p.Trp201Ter Likely pathogenic ★ same condition
- HCCS p.Val103dup Likely pathogenic ★ same condition
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-ala55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown