Is CRIPT p.Lys5Glu (c.13A>G) pathogenic?

CRIPT p.Lys5Glu (c.13A>G) is classified Likely benign in CRIPT (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: ambiguous (0.3451); Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CRIPT p.Lys5Glu (c.13A>G)?

CRIPT p.Lys5Glu (c.13A>G) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CRIPT p.Lys5Glu (c.13A>G) in the general population?

CRIPT p.Lys5Glu (c.13A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CRIPT p.Lys5Glu (c.13A>G)?

AlphaMissense predicts ambiguous (score 0.3451) — an in-silico prediction, not a clinical call.

CRIPT p.Lys5Glu

c.13A>G · rs2466577725 · VCV2681213

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3451 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,555,398)

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
AlphaMissense	0.3451	ambiguous
REVEL	0.301	indeterminate
SaProt	LLR -11.86	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.1	GERP 2, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 6,941 bp · p 0.1 · regional, not allelic
Overall
CADD	25.8	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 1,555,398). 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: CRIPT
Protein: p.Lys5Glu
Coding: c.13A>G
MANE Select: NM_014171
dbSNP: rs2466577725
Type: single nucleotide variant
Location: chr2:46617295 (GRCh38)
Gene constraint: LOEUF 1.852 · pLI 0.19 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.77 · 1 PDB

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

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

CRIPT c.83-1G>A Likely pathogenic ★★ same condition
CRIPT p.Asp92Gly Uncertain significance ★ ⚠ same condition
CRIPT p.Ala45Pro Uncertain significance ★★ ⚠ same type
CRIPT p.Ala84Val Uncertain significance ★★ ⚠ same type
CRIPT p.Cys86Phe Uncertain significance ★★ ⚠ same type
CRIPT p.Gln74Arg Uncertain significance ★★ ⚠ same type
CRIPT p.Gly81Val Uncertain significance ★★ ⚠ same type
CRIPT p.Lys88Arg 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/cript-p-lys5glu (accessed [today's date]).

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