Is CD63 p.Asn129= (c.387C>T) pathogenic?

CD63 p.Asn129= (c.387C>T) is classified Benign in CD63 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-11-20). Common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele.

CD63 p.Asn129=

Q: How common is CD63 p.Asn129= (c.387C>T) in the general population?

CD63 p.Asn129= (c.387C>T) is common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.387C>T · rs13020 · VCV776898

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 7.46%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.51	GERP -1.6, phastCons 0.91
Overall
CADD	6.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 7.46% African / African-American · 5,591/74,962 alleles

Filtering AF 7.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.23%

Overall 0.468% 7,550/1,614,036 alleles · common exomes 4,229/1,461,846 · genomes 3,321/152,190 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	7.46%	13
Admixed American	2.02%	49
Remaining individualsnot grpmax-eligible	0.651%	154
Middle Eastern	0.281%	356
East Asian	0.216%	463
South Asian	0.0428%	2,335
Ashkenazi Jewishnot grpmax-eligible	0.0169%	5,921
European (non-Finnish)	0.0152%	6,592

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: CD63
Protein: p.Asn129=
Coding: c.387C>T
MANE Select: NM_001780
dbSNP: rs13020
Type: single nucleotide variant
Location: chr12:55726739 (GRCh38)
Gene constraint: LOEUF 0.8 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.82 · 2 PDB

Full CD63 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD63 c.426+9G>C Benign ★★ same type
RDH5 c.570-8G>C Benign/Likely benign ★★ same type
CD63 p.Arg108Ser Uncertain significance ★ ⚠ same type
CD63 p.Arg164Gln Uncertain significance ★ ⚠ same type
CD63 p.Asn130His Uncertain significance ★ ⚠ same type
CD63 p.Gln122His Uncertain significance ★ ⚠ same type
CD63 p.Glu189Lys Uncertain significance ★ ⚠ same type
CD63 p.Glu217Lys 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/cd63-p-asn129 (accessed [today's date]).

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