Is CD151 p.Thr120Met (c.359C>T) pathogenic?

CD151 p.Thr120Met (c.359C>T) is classified Uncertain significance in CD151 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-03). AlphaMissense: likely benign (0.1095); Ultra-rare (popmax 0.0866%, afr); Associated with Inborn genetic diseases.

What condition is associated with CD151 p.Thr120Met (c.359C>T)?

CD151 p.Thr120Met (c.359C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CD151 p.Thr120Met (c.359C>T) in the general population?

CD151 p.Thr120Met (c.359C>T) is ultra-rare (popmax 0.0866%, afr) (gnomAD).

What do computational predictors say about CD151 p.Thr120Met (c.359C>T)?

AlphaMissense predicts likely benign (score 0.1095) — an in-silico prediction, not a clinical call.

CD151 p.Thr120Met

c.359C>T · rs34215390 · VCV1429056

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1095 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0866%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1095	likely benign
REVEL	0.146	moderately benign-leaning
SaProt	LLR -5.70	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.42 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.18	GERP -3.4
Regional constraint	o/e 0.94	unconstrained · MANE · 2,119 bp · p 0.3 · regional, not allelic
Overall
CADD	16.83	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 0.0866% African / African-American · 65/75,028 alleles

Filtering AF 0.0697% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0636%

Overall 0.00589% 95/1,612,674 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0866%	1,154
Middle Eastern	0.033%	3,030
East Asian	0.0156%	6,412
Admixed American	0.0117%	8,575
Remaining individualsnot grpmax-eligible	0.00961%	10,411
South Asian	0.0022%	45,537
European (non-Finnish)	0.000509%	196,590

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.Thr120Met
Coding: c.359C>T
MANE Select: NM_004357
dbSNP: rs34215390
Type: single nucleotide variant
Location: chr11:837257 (GRCh38)
Gene constraint: LOEUF 0.816 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.02
Residue 120: a UniProt-annotated variant site (in)

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.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
CD151 p.Ile99Leu 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-thr120met (accessed [today's date]).

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