Is CD151 p.Lys84Asn (c.252G>T) pathogenic?

CD151 p.Lys84Asn (c.252G>T) is classified Conflicting classifications of pathogenicity in CD151 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-19). AlphaMissense: likely pathogenic (0.6743); Low-frequency (popmax 1.12%, afr).

How common is CD151 p.Lys84Asn (c.252G>T) in the general population?

CD151 p.Lys84Asn (c.252G>T) is low-frequency (popmax 1.12%, afr) (gnomAD).

What do computational predictors say about CD151 p.Lys84Asn (c.252G>T)?

AlphaMissense predicts likely pathogenic (score 0.6743) — an in-silico prediction, not a clinical call.

CD151 p.Lys84Asn

c.252G>T · rs116211118 · VCV1554147

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.6743 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.12%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6743	likely pathogenic
REVEL	0.444	indeterminate
SaProt	LLR -9.95	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.5	GERP 0.61, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 2,119 bp · p 0.3 · regional, not allelic
Overall
CADD	24.2	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 1.12% African / African-American · 837/75,050 alleles

Filtering AF 1.05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.03%

Overall 0.0631% 1,016/1,610,334 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.12%	90
Remaining individualsnot grpmax-eligible	0.0913%	1,095
Admixed American	0.0901%	1,110
Middle Eastern	0.0661%	1,514
South Asian	0.00989%	10,114
European (non-Finnish)	0.00466%	21,447

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: CD151
Protein: p.Lys84Asn
Coding: c.252G>T
MANE Select: NM_004357
dbSNP: rs116211118
Type: single nucleotide variant
Location: chr11:836418 (GRCh38)
Gene constraint: LOEUF 0.816 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.02

Full CD151 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD151 p.Lys84Arg Uncertain significance ★★ ⚠ same residue
CD151 p.Lys7Ter Pathogenic ★★ same type
CD151 c.352-11C>G Uncertain significance ★★ same type
CD151 c.702+4A>G Uncertain significance ★★ same type
CD151 c.702+5G>C Uncertain significance ★★ same type
CD151 p.Ala145Thr Uncertain significance ★★ ⚠ same type
CD151 p.Ala81Thr Uncertain significance ★★ ⚠ same type
CD151 p.Arg133Cys 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/cd151-p-lys84asn (accessed [today's date]).

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