Is CD47 p.Lys85Asn (c.255A>T) pathogenic?

CD47 p.Lys85Asn (c.255A>T) is classified Uncertain significance in CD47 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-25). AlphaMissense: likely benign (0.2511); Rare (popmax 0.128%, afr).

How common is CD47 p.Lys85Asn (c.255A>T) in the general population?

CD47 p.Lys85Asn (c.255A>T) is rare (popmax 0.128%, afr) (gnomAD).

What do computational predictors say about CD47 p.Lys85Asn (c.255A>T)?

AlphaMissense predicts likely benign (score 0.2511) — an in-silico prediction, not a clinical call.

CD47 p.Lys85Asn

c.255A>T · rs200864999 · VCV2344986

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2511 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.128%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2511	likely benign
REVEL	0.051	moderately benign-leaning
SaProt	LLR -7.98	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 -0.11	GERP -4.3, phastCons 0.001
Regional constraint	o/e 1.30	unconstrained · MANE · 98 bp · p 0.072 · regional, not allelic
Overall
CADD	9.606	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

Grpmax group 0.128% African / African-American · 96/74,978 alleles

Filtering AF 0.107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0996%

Overall 0.00701% 113/1,613,022 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.128%	781
Admixed American	0.0167%	5,994
Remaining individualsnot grpmax-eligible	0.0112%	8,923

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CD47
Protein: p.Lys85Asn
Coding: c.255A>T
MANE Select: NM_001777
dbSNP: rs200864999
Type: single nucleotide variant
Location: chr3:108080136 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI 0.76 (gnomAD)
Structure: AlphaFold pLDDT 86.48 · 15 PDB
Residue 85: the ig-like v-type domain; a disulfide bond

Full CD47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD47 p.Ala178Gly Uncertain significance ★ ⚠ same type
CD47 p.Ala281Thr Uncertain significance ★ ⚠ same type
CD47 p.Asp104Asn Uncertain significance ★ ⚠ same type
CD47 p.Glu128Lys Uncertain significance ★ ⚠ same type
CD47 p.Gly318Ala Uncertain significance ★ ⚠ same type
CD47 p.Ile127Leu Uncertain significance ★ ⚠ same type
CD47 p.Ile150Val Uncertain significance ★ ⚠ same type
CD47 p.Ile153Val 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/cd47-p-lys85asn (accessed [today's date]).

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