Is CP p.Asp992fs (c.2973dup) pathogenic?

CP p.Asp992fs (c.2973dup) is classified Likely pathogenic in CP (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-01). No gnomAD frequency available for this variant.

How common is CP p.Asp992fs (c.2973dup) in the general population?

CP p.Asp992fs (c.2973dup) is no gnomAD frequency available for this variant (gnomAD).

CP p.Asp992fs

c.2973dup · rs1725520104 · VCV871316

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 17 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1

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.Asp992fs
Coding: c.2973dup
MANE Select: NM_000096
dbSNP: rs1725520104
Type: Duplication
Location: chr3:149177884 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB
Residue 992: the plastocyanin-like 6 domain

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

Similar variants

HPS3 p.Pro992Thr Uncertain significance ★ same residue
CP p.Asp992= Likely benign ★ same residue
HPS3 p.Pro992= Likely benign ★ same residue
HPS3 p.Pro992Ser Uncertain significance same residue
HPS3 p.Arg822fs Pathogenic/Likely pathogenic ★★ same type
HPS3 p.Leu939fs Pathogenic ★★ same type
CP c.2286-14dup Benign ★★ same type
HPS3 c.2887+18_2887+19dup 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/cp-p-asp992fs (accessed [today's date]).

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