Is CD151 p.Asn5= (c.15C>T) pathogenic?

CD151 p.Asn5= (c.15C>T) is classified Likely benign in CD151 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-06). Ultra-rare (popmax 0.02%, afr).

How common is CD151 p.Asn5= (c.15C>T) in the general population?

CD151 p.Asn5= (c.15C>T) is ultra-rare (popmax 0.02%, afr) (gnomAD).

CD151 p.Asn5=

c.15C>T · rs377513403 · VCV2977892

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.02%, afr)

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 -12	GERP -3.8
Overall
CADD	3.645	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.02% African / African-American · 15/74,884 alleles

Filtering AF 0.0123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00989%

Overall 0.00403% 65/1,611,876 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.02%	4,992
Middle Eastern	0.0164%	6,080
Remaining individualsnot grpmax-eligible	0.00641%	15,608
European (non-Finnish)	0.00356%	28,072
East Asian	0.00223%	44,892
Admixed American	0.00167%	59,990
South Asian	0.0011%	91,044

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.Asn5=
Coding: c.15C>T
MANE Select: NM_004357
dbSNP: rs377513403
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

Similar variants

CD151 p.Asn5Lys 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-asn5 (accessed [today's date]).

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