Is CD151 p.Asn5Lys (c.15C>G) pathogenic?

CD151 p.Asn5Lys (c.15C>G) is classified Uncertain significance in CD151 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-14). AlphaMissense: likely benign (0.0919); Very rare (popmax 0.0017%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CD151 p.Asn5Lys (c.15C>G)?

CD151 p.Asn5Lys (c.15C>G) is associated with Inborn genetic diseases (ClinVar).

How common is CD151 p.Asn5Lys (c.15C>G) in the general population?

CD151 p.Asn5Lys (c.15C>G) is very rare (popmax 0.0017%, nfe) (gnomAD).

What do computational predictors say about CD151 p.Asn5Lys (c.15C>G)?

AlphaMissense predicts likely benign (score 0.0919) — an in-silico prediction, not a clinical call.

CD151 p.Asn5Lys

c.15C>G · VCV3487802

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0919 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0017%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0919	likely benign
REVEL	0.015	strongly benign-leaning
SaProt	LLR -4.87	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 -12	GERP -3.8
Regional constraint	o/e 0.94	unconstrained · MANE · 2,119 bp · p 0.3 · regional, not allelic
Overall
CADD	0.006	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 0.0017% European (non-Finnish) · 20/1,179,028 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.0013% 21/1,611,876 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0017%	58,951
Remaining individualsnot grpmax-eligible	0.0016%	62,434

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.Asn5Lys
Coding: c.15C>G
MANE Select: NM_004357
Type: single nucleotide variant
Location: chr11:836084 (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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD151 p.Asn5= Likely benign ★ same residue
CD151 p.Ala145Thr Uncertain significance ★★ ⚠ same condition
CD151 p.Arg86His Uncertain significance ★★ ⚠ same condition
CD151 p.Arg91Cys Uncertain significance ★★ ⚠ same condition
CD151 p.Asp147Asn Uncertain significance ★★ ⚠ same condition
CD151 p.Gly55Asp Uncertain significance ★★ ⚠ same condition
CD151 p.His139Tyr Uncertain significance ★★ ⚠ same condition
CD151 p.Ile49Val Uncertain significance ★★ ⚠ same condition

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-asn5lys (accessed [today's date]).

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