Is CDCP1 p.Glu293Lys (c.877G>A) pathogenic?

CDCP1 p.Glu293Lys (c.877G>A) is classified Uncertain significance in CDCP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-15). AlphaMissense: likely pathogenic (0.7251); Rare (popmax 0.104%, nfe).

How common is CDCP1 p.Glu293Lys (c.877G>A) in the general population?

CDCP1 p.Glu293Lys (c.877G>A) is rare (popmax 0.104%, nfe) (gnomAD).

What do computational predictors say about CDCP1 p.Glu293Lys (c.877G>A)?

AlphaMissense predicts likely pathogenic (score 0.7251) — an in-silico prediction, not a clinical call.

CDCP1 p.Glu293Lys

c.877G>A · rs144577185 · VCV3141053

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7251 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.104%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7251	likely pathogenic
REVEL	0.312	indeterminate
SaProt	LLR -5.13	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 27 kb · p 7.2e-12 · regional, not allelic
Overall
CADD	27.5	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 0.104% European (non-Finnish) · 1,233/1,180,030 alleles

Filtering AF 0.0996% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0976%

Overall 0.082% 1,323/1,614,184 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.104%	957
Remaining individualsnot grpmax-eligible	0.072%	1,389
Middle Eastern	0.033%	3,031
Admixed American	0.025%	4,001
Finnishnot grpmax-eligible	0.0187%	5,336
Ashkenazi Jewishnot grpmax-eligible	0.0169%	5,921
African / African-American	0.0147%	6,822

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: CDCP1
Protein: p.Glu293Lys
Coding: c.877G>A
MANE Select: NM_022842
dbSNP: rs144577185
Type: single nucleotide variant
Location: chr3:45110620 (GRCh38)
Gene constraint: LOEUF 0.601 · pLI 0.05 (gnomAD)
Structure: AlphaFold pLDDT 78.13

Full CDCP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCP1 p.Glu293Gly Uncertain significance ★ ⚠ same residue
CDCP1 p.Ala306= Benign ★★ same type
CDCP1 p.Arg763Gln Benign ★★ same type
CDCP1 p.Gly596Ser Benign ★★ ⚠ same type
CDCP1 p.Ala212Val Uncertain significance ★ ⚠ same type
CDCP1 p.Ala320Thr Uncertain significance ★ ⚠ same type
CDCP1 p.Ala464Gly Uncertain significance ★ ⚠ same type
CDCP1 p.Ala521Gly 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/cdcp1-p-glu293lys (accessed [today's date]).

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