Is CD151 p.Leu98= (c.294C>T) pathogenic?

CD151 p.Leu98= (c.294C>T) is classified Likely benign in CD151 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-04-10). Very rare (popmax 0.00525%, nfe).

How common is CD151 p.Leu98= (c.294C>T) in the general population?

CD151 p.Leu98= (c.294C>T) is very rare (popmax 0.00525%, nfe) (gnomAD).

CD151 p.Leu98=

c.294C>T · rs144204595 · VCV2173161

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00525%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.26	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -2.1	GERP -4.4
Overall
CADD	7.647	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00525% European (non-Finnish) · 62/1,179,928 alleles

Filtering AF 0.00418% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0038%

Overall 0.0044% 71/1,612,662 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0112%	8,923
European (non-Finnish)grpmax	0.00525%	19,031
Admixed American	0.00333%	29,992

Remaining individuals 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.Leu98=
Coding: c.294C>T
MANE Select: NM_004357
dbSNP: rs144204595
Type: single nucleotide variant
Location: chr11:836786 (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.Leu98del 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-leu98 (accessed [today's date]).

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