Is CD320 p.Asp160Tyr (c.478G>T) pathogenic?

CD320 p.Asp160Tyr (c.478G>T) is classified Uncertain significance in CD320 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-03). AlphaMissense: likely pathogenic (0.839); Absent from gnomAD v4.1.

How common is CD320 p.Asp160Tyr (c.478G>T) in the general population?

CD320 p.Asp160Tyr (c.478G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD320 p.Asp160Tyr (c.478G>T)?

AlphaMissense predicts likely pathogenic (score 0.839) — an in-silico prediction, not a clinical call.

CD320 p.Asp160Tyr

c.478G>T · VCV4222858

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.839 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,604,342)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.839	likely pathogenic
REVEL	0.414	indeterminate
SaProt	LLR -14.10	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -0.3, phastCons 0.88
Regional constraint	o/e 1.03	unconstrained · MANE · 5,824 bp · p 0.57 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

No allele count reported in gnomAD v4.1 (AN 1,604,342). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CD320
Protein: p.Asp160Tyr
Coding: c.478G>T
MANE Select: NM_016579
Type: single nucleotide variant
Location: chr19:8303879 (GRCh38)
Gene constraint: LOEUF 1.488 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.61 · 6 PDB
Residue 160: a disulfide bond; the ldl-receptor class a 2 domain

Full CD320 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD320 p.Asp160Asn Uncertain significance ★★ ⚠ same residue
CD320 p.Arg129Leu Uncertain significance ★★ ⚠ same type
CD320 p.Arg138Ser Uncertain significance ★★ ⚠ same type
CD320 p.Arg254Gln Uncertain significance ★★ ⚠ same type
CD320 p.Arg258His Uncertain significance ★★ ⚠ same type
CD320 p.Asn170Ser Uncertain significance ★★ ⚠ same type
CD320 p.Asp143Asn Uncertain significance ★★ ⚠ same type
CD320 p.Gly166Val 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/cd320-p-asp160tyr (accessed [today's date]).

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