Is CD27 p.Thr143= (c.429C>T) pathogenic?

CD27 p.Thr143= (c.429C>T) is classified Likely benign in CD27 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-05). Absent from gnomAD v4.1.

How common is CD27 p.Thr143= (c.429C>T) in the general population?

CD27 p.Thr143= (c.429C>T) is absent from gnomAD v4.1 (gnomAD).

CD27 p.Thr143=

c.429C>T · rs1592122473 · VCV756311

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.009	GERP -1.2
Overall
CADD	8.158	PHRED · no single calibrated threshold — expert panels disagree

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: CD27
Protein: p.Thr143=
Coding: c.429C>T
MANE Select: NM_001242
dbSNP: rs1592122473
Type: single nucleotide variant
Location: chr12:6450333 (GRCh38)
Gene constraint: LOEUF 0.946 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 71.79 · 5 PDB

Full CD27 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD27 p.Cys53Tyr Pathogenic ★★ same type
CD27 p.Ala164Pro Uncertain significance ★★ ⚠ same type
CD27 p.Ala229Thr Uncertain significance ★★ ⚠ same type
CD27 p.Arg155Thr Uncertain significance ★★ ⚠ same type
CD27 p.Arg172Gln Uncertain significance ★★ ⚠ same type
CD27 p.Arg172Gly Uncertain significance ★★ ⚠ same type
CD27 p.Arg182Ser Uncertain significance ★★ ⚠ same type
CD27 p.Arg238Lys 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/cd27-p-thr143 (accessed [today's date]).

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