Is CCN4 p.Pro170Leu (c.509C>T) pathogenic?

CCN4 p.Pro170Leu (c.509C>T) is classified Uncertain significance in CCN4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-07). AlphaMissense: likely benign (0.2851); Ultra-rare (popmax 0.0671%, mid).

How common is CCN4 p.Pro170Leu (c.509C>T) in the general population?

CCN4 p.Pro170Leu (c.509C>T) is ultra-rare (popmax 0.0671%, mid) (gnomAD).

What do computational predictors say about CCN4 p.Pro170Leu (c.509C>T)?

AlphaMissense predicts likely benign (score 0.2851) — an in-silico prediction, not a clinical call.

CCN4 p.Pro170Leu

c.509C>T · rs139058011 · VCV3139814

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2851 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0671%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2851	likely benign
REVEL	0.572	indeterminate
SaProt	LLR -12.24	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 1.9, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 37 kb · p 1 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0671% Middle Eastern · 4/5,962 alleles

Filtering AF 0.0229% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0172%

Overall 0.011% 178/1,613,580 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0671%	1,490
Admixed American	0.0317%	3,159
African / African-American	0.0147%	6,824
Remaining individualsnot grpmax-eligible	0.0128%	7,812
European (non-Finnish)	0.011%	9,077
South Asian	0.00549%	18,212
East Asian	0.00223%	44,866

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CCN4
Protein: p.Pro170Leu
Coding: c.509C>T
MANE Select: NM_003882
dbSNP: rs139058011
Type: single nucleotide variant
Location: chr8:133220740 (GRCh38)
Gene constraint: LOEUF 1.151 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.16
Residue 170: the vwfc domain

Full CCN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCN4 p.Arg97= Benign ★★ same type
CCN4 p.Leu99= Benign ★★ same type
CCN4 p.Thr145Met Likely benign ★★ ⚠ same type
CCN4 p.Ala10Glu Uncertain significance ★ ⚠ same type
CCN4 p.Ala10Thr Uncertain significance ★ ⚠ same type
CCN4 p.Ala17Ser Uncertain significance ★ ⚠ same type
CCN4 p.Ala196Thr Uncertain significance ★ ⚠ same type
CCN4 p.Ala243Ser Uncertain significance ★ ⚠ 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/ccn4-p-pro170leu (accessed [today's date]).

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