Is CD247 p.Phe24Cys (c.71T>G) pathogenic?

CD247 p.Phe24Cys (c.71T>G) is classified Likely benign in CD247 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.3082); Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CD247 p.Phe24Cys (c.71T>G)?

CD247 p.Phe24Cys (c.71T>G) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CD247 p.Phe24Cys (c.71T>G) in the general population?

CD247 p.Phe24Cys (c.71T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD247 p.Phe24Cys (c.71T>G)?

AlphaMissense predicts likely benign (score 0.3082) — an in-silico prediction, not a clinical call.

CD247 p.Phe24Cys

c.71T>G · rs2524512603 · VCV2681708

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3082 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
AlphaMissense	0.3082	likely benign
REVEL	0.311	indeterminate
SaProt	LLR -8.79	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP -1.2, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 87 kb · p 0.18 · regional, not allelic
Overall
CADD	24.1	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: CD247
Protein: p.Phe24Cys
Coding: c.71T>G
MANE Select: NM_198053
dbSNP: rs2524512603
Type: single nucleotide variant
Location: chr1:167440755 (GRCh38)
Gene constraint: LOEUF 0.633 · pLI 0.66 (gnomAD)
Structure: AlphaFold pLDDT 62.36 · 38 PDB

Full CD247 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

CD247 p.Gln101Ter Pathogenic/Likely pathogenic ★★ same condition
CD247 p.Ile18fs Pathogenic/Likely pathogenic ★★ same condition
CD247 p.Lys136fs Likely pathogenic ★ same condition
CD247 c.58+6G>T Uncertain significance ★★ same type
CD247 p.Ala120Val Uncertain significance ★★ ⚠ same type
CD247 p.Ala63Pro Uncertain significance ★★ ⚠ same type
CD247 p.Ala9Thr Uncertain significance ★★ ⚠ same type
CD247 p.Arg103Lys 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/cd247-p-phe24cys (accessed [today's date]).

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