Is CFP p.Arg161Ter (c.481C>T) pathogenic?

CFP p.Arg161Ter (c.481C>T) is classified Pathogenic in CFP (ClinVar, Single submitter, 2 submitters; last evaluated 2024-04-25). Absent from gnomAD v4.1; Associated with properdin deficiency, X-linked.

What condition is associated with CFP p.Arg161Ter (c.481C>T)?

CFP p.Arg161Ter (c.481C>T) is associated with properdin deficiency, X-linked (ClinVar).

How common is CFP p.Arg161Ter (c.481C>T) in the general population?

CFP p.Arg161Ter (c.481C>T) is absent from gnomAD v4.1 (gnomAD).

How is Properdin deficiency inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CFP p.Arg161Ter

c.481C>T · rs132630258 · VCV11181

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

properdin deficiency, X-linked

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 9
Splicing
SpliceAI	Δ0.96	donor gain · deltas
Pangolin	Δ0.78	gain · loss 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 4.6	GERP -1.9, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFP
Protein: p.Arg161Ter
Coding: c.481C>T
MANE Select: NM_001145252
dbSNP: rs132630258
Type: single nucleotide variant
Location: chrX:47627564 (GRCh38)
Structure: AlphaFold pLDDT 83.75 · 14 PDB
Residue 161: the tsp type-1 2 domain

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

Disease context

properdin deficiency, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Properdin deficiency (Orphanet):

Inheritance: X-linked recessive

Similar variants

CFP p.Arg161Gln Uncertain significance ★ ⚠ same residue
CFP p.Arg157Gln Uncertain significance ★★ ⚠ same condition
CFP p.Glu215Lys Uncertain significance ★★ ⚠ same condition
CFP p.Gly41Ser Benign/Likely benign ★★ same condition
CFP c.767-2A>T Likely pathogenic ★ same condition
CFP p.Ala242Ser Uncertain significance ★ ⚠ same condition
CFP p.Arg159His Conflicting classifications of pathogenicity ★ ⚠ same condition
CFP p.Pro134Ser Uncertain significance ★ ⚠ 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/cfp-p-arg161ter (accessed [today's date]).

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