Is CDCP1 p.Gly596Ser (c.1786G>A) pathogenic?

CDCP1 p.Gly596Ser (c.1786G>A) is classified Benign in CDCP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-24). AlphaMissense: likely benign (0.0923); Low-frequency (popmax 3.48%, afr).

How common is CDCP1 p.Gly596Ser (c.1786G>A) in the general population?

CDCP1 p.Gly596Ser (c.1786G>A) is low-frequency (popmax 3.48%, afr) (gnomAD).

What do computational predictors say about CDCP1 p.Gly596Ser (c.1786G>A)?

AlphaMissense predicts likely benign (score 0.0923) — an in-silico prediction, not a clinical call.

CDCP1 p.Gly596Ser

c.1786G>A · rs35353149 · VCV712052

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0923 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.48%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0923	likely benign
REVEL	0.16	moderately benign-leaning
SaProt	LLR -8.60	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -0.96, phastCons 0.78
Regional constraint	o/e 0.78	unconstrained · MANE · 27 kb · p 7.2e-12 · regional, not allelic
Overall
CADD	19.62	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 3.48% African / African-American · 2,614/75,018 alleles

Filtering AF 3.37% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.33%

Overall 0.226% 3,651/1,614,134 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.48%	29
Middle Eastern	0.396%	253
Admixed American	0.368%	272
Remaining individualsnot grpmax-eligible	0.336%	298
Ashkenazi Jewishnot grpmax-eligible	0.118%	846
European (non-Finnish)	0.0453%	2,210
South Asian	0.0132%	7,590
Finnishnot grpmax-eligible	0.00156%	64,016

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.Gly596Ser
Coding: c.1786G>A
MANE Select: NM_022842
dbSNP: rs35353149
Type: single nucleotide variant
Location: chr3:45091380 (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.Ala306= Benign ★★ same type
CDCP1 p.Arg763Gln 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
CDCP1 p.Ala528Ser Uncertain significance ★ ⚠ same type
CDCP1 p.Ala604Thr 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-gly596ser (accessed [today's date]).

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