Is CP p.Ala17fs (c.48del) pathogenic?

CP p.Ala17fs (c.48del) is classified Likely pathogenic in CP (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-01). Absent from gnomAD.

How common is CP p.Ala17fs (c.48del) in the general population?

CP p.Ala17fs (c.48del) is absent from gnomAD (gnomAD).

CP p.Ala17fs

c.48del · rs1553765380 · VCV546950

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 1 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP 0.11, phastCons 0.98

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CP
Protein: p.Ala17fs
Coding: c.48del
MANE Select: NM_000096
dbSNP: rs1553765380
Type: Deletion
Location: chr3:149221745 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB

Full CP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CP c.607+1del Pathogenic/Likely pathogenic ★★ same type
CP p.Pro689fs Pathogenic/Likely pathogenic ★★ same type
HPS3 c.2796+1del Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Ile807_Trp808insTer Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Leu911_Leu912insTer Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Phe781fs Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Phe800fs Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Thr773fs Pathogenic/Likely pathogenic ★★ 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/cp-p-ala17fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown