Is CDCP2 c.1117+97C>T pathogenic?

CDCP2 c.1117+97C>T is classified Uncertain significance in CDCP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-07). AlphaMissense: likely benign (0.0954); Very rare (popmax 0.0033%, sas).

How common is CDCP2 c.1117+97C>T in the general population?

CDCP2 c.1117+97C>T is very rare (popmax 0.0033%, sas) (gnomAD).

What do computational predictors say about CDCP2 c.1117+97C>T?

AlphaMissense predicts likely benign (score 0.0954) — an in-silico prediction, not a clinical call.

CDCP2 c.1117+97C>T

VCV3998744

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0954 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0033%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0954	likely benign
REVEL	0.059	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
Splice region	donor +97	deep intronic (+97 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.043	GERP -2.4, phastCons 0.62
Non-coding constraint	Z 2.24	1 kb window · o/e 0.80 · regional · uncalibrated
Overall
CADD	7.411	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0033% South Asian · 3/90,776 alleles

Filtering AF 0.000878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000342% 5/1,460,024 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0033%	30,259
Remaining individualsnot grpmax-eligible	0.0016%	62,444
European (non-Finnish)	8.48e-05%	1,178,756

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: CDCP2
Coding: c.1117+97C>T
MANE Select: NM_001353655
Type: single nucleotide variant
Location: chr1:54139656 (GRCh38)
Gene constraint: LOEUF 1.369 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.43

Full CDCP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCP2 c.1117+105C>T Uncertain significance ★ ⚠ same type
CDCP2 c.1117+106C>T Uncertain significance ★ ⚠ same type
CDCP2 c.1117+10G>A Uncertain significance ★ ⚠ same type
CDCP2 c.1117+110G>T Uncertain significance ★ ⚠ same type
CDCP2 c.1117+15G>A Uncertain significance ★ ⚠ same type
CDCP2 c.1117+168C>G Uncertain significance ★ ⚠ same type
CDCP2 c.1117+184C>T Uncertain significance ★ ⚠ same type
CDCP2 p.Ala138Thr 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/cdcp2-c-1117-plus-97c-t (accessed [today's date]).

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