Is CD72 p.Asp359His (c.1075G>C) pathogenic?

CD72 p.Asp359His (c.1075G>C) is classified Uncertain significance in CD72 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-19). AlphaMissense: ambiguous (0.4491); Absent from gnomAD v4.1.

How common is CD72 p.Asp359His (c.1075G>C) in the general population?

CD72 p.Asp359His (c.1075G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD72 p.Asp359His (c.1075G>C)?

AlphaMissense predicts ambiguous (score 0.4491) — an in-silico prediction, not a clinical call.

CD72 p.Asp359His

c.1075G>C · VCV3264872

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4491 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4491	ambiguous
REVEL	0.205	benign-leaning
SaProt	LLR -5.99	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -1.3, phastCons 0.078
Regional constraint	o/e 0.96	unconstrained · MANE · 7,676 bp · p 0.39 · regional, not allelic
Overall
CADD	18.81	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: CD72
Protein: p.Asp359His
Coding: c.1075G>C
MANE Select: NM_001782
Type: single nucleotide variant
Location: chr9:35610629 (GRCh38)
Gene constraint: LOEUF 0.832 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.85

Full CD72 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD72 p.Ala180Glu Uncertain significance ★ ⚠ same type
CD72 p.Ala269Val Uncertain significance ★ ⚠ same type
CD72 p.Ala2Gly Uncertain significance ★ ⚠ same type
CD72 p.Ala4Thr Uncertain significance ★ ⚠ same type
CD72 p.Ala81Val Uncertain significance ★ ⚠ same type
CD72 p.Arg144Cys Uncertain significance ★ ⚠ same type
CD72 p.Arg161Lys Uncertain significance ★ ⚠ same type
CD72 p.Arg84Leu 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/cd72-p-asp359his (accessed [today's date]).

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