Is CITED2 p.Ala7Pro (c.19G>C) pathogenic?

CITED2 p.Ala7Pro (c.19G>C) is classified Uncertain significance in CITED2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-21). AlphaMissense: likely pathogenic (0.8561); Absent from gnomAD v4.1.

How common is CITED2 p.Ala7Pro (c.19G>C) in the general population?

CITED2 p.Ala7Pro (c.19G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CITED2 p.Ala7Pro (c.19G>C)?

AlphaMissense predicts likely pathogenic (score 0.8561) — an in-silico prediction, not a clinical call.

CITED2 p.Ala7Pro

c.19G>C · rs2482760779 · VCV2446089

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8561 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8561	likely pathogenic
REVEL	0.25	benign-leaning
SaProt	LLR -7.47	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.5, phastCons 1
Regional constraint	o/e 1.22	unconstrained · MANE · 659 bp · p 8.7e-05 · regional, not allelic
Overall
CADD	23.5	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CITED2
Protein: p.Ala7Pro
Coding: c.19G>C
MANE Select: NM_006079
dbSNP: rs2482760779
Type: single nucleotide variant
Location: chr6:139373926 (GRCh38)
Gene constraint: LOEUF 0.588 · pLI 0.90 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 52.07 · 4 PDB

Full CITED2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CITED2 p.Ala7= Benign ★★ same residue
CITED2 p.Ala7Val Uncertain significance ★ ⚠ same residue
CITED2 p.Ala25Pro Uncertain significance ★★ ⚠ same type
CITED2 p.Ala25Val Uncertain significance ★★ ⚠ same type
CITED2 p.Pro128Ser Uncertain significance ★★ ⚠ same type
CITED2 p.Gly194= Benign/Likely benign ★★ same type
CITED2 p.His160Leu Benign/Likely benign ★★ same type
CITED2 p.His46= Likely benign ★★ 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/cited2-p-ala7pro (accessed [today's date]).

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