Is PROC c.796+16del pathogenic?

PROC c.796+16del is classified Likely benign in PROC (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-24). Associated with thrombophilia due to protein C deficiency, autosomal dominant.

What condition is associated with PROC c.796+16del?

PROC c.796+16del is associated with thrombophilia due to protein C deficiency, autosomal dominant (ClinVar).

PROC c.796+16del

Q: How is Severe hereditary thrombophilia due to congenital protein C deficiency inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

VCV4805400

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

thrombophilia due to protein C deficiency, autosomal dominant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +16	near-intronic (+16 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.61
Non-coding constraint	Z 3.45	1 kb window · o/e 0.73 · regional · uncalibrated

Variant & gene context

Gene: PROC
Coding: c.796+16del
MANE Select: NM_000312
Type: Deletion
Location: chr2:127427238 (GRCh38)
Gene constraint: LOEUF 0.894 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.35 · 12 PDB

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

Disease context

thrombophilia due to protein C deficiency, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Severe hereditary thrombophilia due to congenital protein C deficiency (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Neonatal
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

PROC p.Leu303fs Pathogenic/Likely pathogenic ★★ same condition
PROC p.Asp113_Ile115del Uncertain significance ★ same condition
PROC p.Ser119_Ser124del Conflicting classifications of pathogenicity ★ same condition
PROC p.Val434_Tyr435insTer Uncertain significance ★ same condition
PROC c.400+9del Benign ★ same condition
PROC p.Gly423fs Pathogenic same condition
PROC p.Ala309Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
PROC p.Arg199Ter 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/proc-c-796-plus-16del (accessed [today's date]).

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