Is CDIP1 p.Tyr155= (c.465C>T) pathogenic?

CDIP1 p.Tyr155= (c.465C>T) is classified Likely benign in CDIP1 (ClinVar, No assertion criteria, 1 submitter). Ultra-rare (popmax 0.0119%, eas); Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CDIP1 p.Tyr155= (c.465C>T)?

CDIP1 p.Tyr155= (c.465C>T) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CDIP1 p.Tyr155= (c.465C>T) in the general population?

CDIP1 p.Tyr155= (c.465C>T) is ultra-rare (popmax 0.0119%, eas) (gnomAD).

CDIP1 p.Tyr155=

c.465C>T · rs370972341 · VCV2681711

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0119%, eas)

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.8	GERP -3.4
Overall
CADD	4.8	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0119% East Asian · 5/42,142 alleles

Filtering AF 0.00467% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00301%

Overall 0.00141% 22/1,563,032 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0119%	8,428
Ashkenazi Jewishnot grpmax-eligible	0.00697%	14,356
African / African-American	0.00406%	24,622
Remaining individualsnot grpmax-eligible	0.0033%	30,321
Admixed American	0.00194%	51,516
South Asian	0.00117%	85,498
European (non-Finnish)	0.000694%	144,121

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: CDIP1
Protein: p.Tyr155=
Coding: c.465C>T
MANE Select: NM_013399
dbSNP: rs370972341
Type: single nucleotide variant
Location: chr16:4512841 (GRCh38)
Gene constraint: LOEUF 1.142 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.37
Residue 155: the litaf domain

Full CDIP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

CDIP1 p.Ala122Thr Uncertain significance ★ ⚠ same type
CDIP1 p.Ala136Ser Uncertain significance ★ ⚠ same type
CDIP1 p.Ala34Gly Uncertain significance ★ ⚠ same type
CDIP1 p.Arg30His Uncertain significance ★ ⚠ same type
CDIP1 p.Asp48Asn Uncertain significance ★ ⚠ same type
CDIP1 p.Asp74His Uncertain significance ★ ⚠ same type
CDIP1 p.Gln37Leu Uncertain significance ★ ⚠ same type
CDIP1 p.Gly172Arg 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/cdip1-p-tyr155 (accessed [today's date]).

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