Is CDX2 p.Asp112Asn (c.334G>A) pathogenic?

CDX2 p.Asp112Asn (c.334G>A) is classified Uncertain significance in CDX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-03). AlphaMissense: ambiguous (0.4044); Very rare (popmax 0.00279%, afr).

How common is CDX2 p.Asp112Asn (c.334G>A) in the general population?

CDX2 p.Asp112Asn (c.334G>A) is very rare (popmax 0.00279%, afr) (gnomAD).

What do computational predictors say about CDX2 p.Asp112Asn (c.334G>A)?

AlphaMissense predicts ambiguous (score 0.4044) — an in-silico prediction, not a clinical call.

CDX2 p.Asp112Asn

c.334G>A · rs1345464021 · VCV2314899

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4044 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00279%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4044	ambiguous
REVEL	0.094	moderately benign-leaning
SaProt	LLR -6.46	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP 1, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 505 bp · p 0.73 · regional, not allelic
Overall
CADD	21.6	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 0.00279% African / African-American · 2/71,690 alleles

Filtering AF 0.000463% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000173%

Overall 0.000196% 3/1,533,594 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00279%	35,845
Admixed American	0.00198%	50,568

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: CDX2
Protein: p.Asp112Asn
Coding: c.334G>A
MANE Select: NM_001265
dbSNP: rs1345464021
Type: single nucleotide variant
Location: chr13:27968673 (GRCh38)
Gene constraint: LOEUF 0.609 · pLI 0.79 (gnomAD)
Structure: AlphaFold pLDDT 63.77 · 4 PDB

Full CDX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDX2 p.Asp112Ala Uncertain significance ★ ⚠ same residue
CDX2 p.Ter314Arg Likely pathogenic ★ same type
CDX2 p.Ala103Ser Uncertain significance ★ ⚠ same type
CDX2 p.Ala127Asp Uncertain significance ★ ⚠ same type
CDX2 p.Ala148Ser Uncertain significance ★ ⚠ same type
CDX2 p.Ala46Glu Uncertain significance ★ ⚠ same type
CDX2 p.Ala68Gly Uncertain significance ★ ⚠ same type
CDX2 p.Ala86Ser 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/cdx2-p-asp112asn (accessed [today's date]).

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