Is CD151 p.Thr10del (c.24_26del) pathogenic?

CD151 p.Thr10del (c.2426del) is classified Uncertain significance in CD151 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-18). Ultra-rare (popmax 0.011%, sas).

How common is CD151 p.Thr10del (c.24_26del) in the general population?

CD151 p.Thr10del (c.24_26del) is ultra-rare (popmax 0.011%, sas) (gnomAD).

CD151 p.Thr10del

c.24_26del · rs780763258 · VCV1917762

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.011%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP 1.6, phastCons 0.91
Overall
CADD	12.48	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.011% South Asian · 10/91,074 alleles

Filtering AF 0.00594% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00453%

Overall 0.00298% 48/1,612,650 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0811%	1,234
South Asiangrpmax	0.011%	9,107
Remaining individualsnot grpmax-eligible	0.0064%	15,615
Admixed American	0.005%	20,000
European (non-Finnish)	0.000593%	168,524

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Thr10del
Coding: c.24_26del
MANE Select: NM_004357
dbSNP: rs780763258
Type: Deletion
Location: chr11:836093 (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.Cys208_Thr210del Likely pathogenic ★ same type
CD151 c.616-42_616-11del Uncertain significance ★ same type
CD151 p.Gly176fs Uncertain significance ★ same type
CD151 c.276+107del Benign ★ same type
CD151 c.277-3del Benign ★ same type
CD151 c.615+44del Benign ★ same type
CD151 c.615+51del Benign ★ 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-thr10del (accessed [today's date]).

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