Is CD164 p.Thr55Ser (c.163A>T) pathogenic?

CD164 p.Thr55Ser (c.163A>T) is classified Likely benign in CD164 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.0951); Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CD164 p.Thr55Ser (c.163A>T)?

CD164 p.Thr55Ser (c.163A>T) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CD164 p.Thr55Ser (c.163A>T) in the general population?

CD164 p.Thr55Ser (c.163A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD164 p.Thr55Ser (c.163A>T)?

AlphaMissense predicts likely benign (score 0.0951) — an in-silico prediction, not a clinical call.

CD164 p.Thr55Ser

c.163A>T · rs2482473942 · VCV2681707

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0951 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
AlphaMissense	0.0951	likely benign
REVEL	0.061	moderately benign-leaning
SaProt	LLR -7.50	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.5	GERP -2.2
Regional constraint	o/e 1.21	unconstrained · MANE · 14 kb · p 0.001 · regional, not allelic
Overall
CADD	13.33	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: CD164
Protein: p.Thr55Ser
Coding: c.163A>T
MANE Select: NM_006016
dbSNP: rs2482473942
Type: single nucleotide variant
Location: chr6:109382216 (GRCh38)
Gene constraint: LOEUF 1.232 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 67.15

Full CD164 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

CD164 p.Thr55Ile Uncertain significance ★ ⚠ same residue
CD164 p.Leu9Phe Uncertain significance ★★ ⚠ same condition
CD164 c.332-4A>G Uncertain significance ★ same condition
CD164 c.175+631C>T Benign same condition
CD164 c.*533A>T Likely benign same condition
CD164 p.Arg192Ter Uncertain significance ★★ same type
CD164 p.Asn121Ser Uncertain significance ★★ ⚠ same type
CD164 p.Asn32Lys 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/cd164-p-thr55ser (accessed [today's date]).

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