Is CD52 p.Val17Leu (c.49G>C) pathogenic?

CD52 p.Val17Leu (c.49G>C) is classified Uncertain significance in CD52 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-14). AlphaMissense: likely benign (0.183); Absent from gnomAD v4.1.

How common is CD52 p.Val17Leu (c.49G>C) in the general population?

CD52 p.Val17Leu (c.49G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD52 p.Val17Leu (c.49G>C)?

AlphaMissense predicts likely benign (score 0.183) — an in-silico prediction, not a clinical call.

CD52 p.Val17Leu

c.49G>C · rs2523814040 · VCV2237260

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.183 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.183	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -5.74	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 0.49	GERP -3.8
Regional constraint	o/e 0.82	unconstrained · MANE · 2,281 bp · p 0.11 · regional, not allelic
Overall
CADD	9.808	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: CD52
Protein: p.Val17Leu
Coding: c.49G>C
MANE Select: NM_001803
dbSNP: rs2523814040
Type: single nucleotide variant
Location: chr1:26318066 (GRCh38)
Gene constraint: LOEUF 1.787 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 68.22 · 1 PDB

Full CD52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD52 p.Arg3Cys Uncertain significance ★ ⚠ same type
CD52 p.Cys59Gly Uncertain significance ★ ⚠ same type
CD52 p.Gly43Arg Uncertain significance ★ ⚠ same type
CD52 p.Ile11Val Uncertain significance ★ ⚠ same type
CD52 p.Leu5Val Uncertain significance ★ ⚠ same type
CD52 p.Met16Thr Uncertain significance ★ ⚠ same type
CD52 p.Val15Leu Uncertain significance ★ ⚠ same type
CD52 p.Val50Met 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/cd52-p-val17leu (accessed [today's date]).

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