Is CITED2 p.Met5Val (c.13A>G) pathogenic?

CITED2 p.Met5Val (c.13A>G) is classified Uncertain significance in CITED2 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: ambiguous (0.4706); Absent from gnomAD v4.1.

How common is CITED2 p.Met5Val (c.13A>G) in the general population?

CITED2 p.Met5Val (c.13A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CITED2 p.Met5Val (c.13A>G)?

AlphaMissense predicts ambiguous (score 0.4706) — an in-silico prediction, not a clinical call.

CITED2 p.Met5Val

c.13A>G · rs1778320748 · VCV1050048

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4706 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,598,710)

Computational evidence

Protein change
AlphaMissense	0.4706	ambiguous
REVEL	0.383	indeterminate
SaProt	LLR -7.52	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.5, phastCons 1
Regional constraint	o/e 1.22	unconstrained · MANE · 659 bp · p 8.7e-05 · regional, not allelic
Overall
CADD	22.9	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

No allele count reported in gnomAD v4.1 (AN 1,598,710). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CITED2
Protein: p.Met5Val
Coding: c.13A>G
MANE Select: NM_006079
dbSNP: rs1778320748
Type: single nucleotide variant
Location: chr6:139373932 (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.Met5Thr 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.Ala7= Benign ★★ 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-met5val (accessed [today's date]).

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