Is CD47 p.Met319Val (c.955A>G) pathogenic?

CD47 p.Met319Val (c.955A>G) is classified Uncertain significance in CD47 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-15). AlphaMissense: ambiguous (0.5399); Very rare (popmax 0.000516%, nfe).

How common is CD47 p.Met319Val (c.955A>G) in the general population?

CD47 p.Met319Val (c.955A>G) is very rare (popmax 0.000516%, nfe) (gnomAD).

What do computational predictors say about CD47 p.Met319Val (c.955A>G)?

AlphaMissense predicts ambiguous (score 0.5399) — an in-silico prediction, not a clinical call.

CD47 p.Met319Val

c.955A>G · VCV3488105

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5399 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000516%, nfe)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5399	ambiguous
REVEL	0.208	benign-leaning
SaProt	LLR -5.71	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 7.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 12 kb · p 0.71 · regional, not allelic
Overall
CADD	22.5	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

Grpmax group 0.000516% European (non-Finnish) · 6/1,161,982 alleles

Filtering AF 0.000186% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000122%

Overall 0.000376% 6/1,594,096 alleles · very rare

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.Met319Val
Coding: c.955A>G
MANE Select: NM_001777
Type: single nucleotide variant
Location: chr3:108049631 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI 0.76 (gnomAD)
Structure: AlphaFold pLDDT 86.48 · 15 PDB

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

Similar variants

CD47 p.Met319Arg Uncertain significance ★ ⚠ same residue
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

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-met319val (accessed [today's date]).

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