Is CD151 p.His139Tyr (c.415C>T) pathogenic?

CD151 p.His139Tyr (c.415C>T) is classified Uncertain significance in CD151 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-28). AlphaMissense: likely benign (0.1139); Ultra-rare (popmax 0.0164%, mid); Associated with Inborn genetic diseases.

What condition is associated with CD151 p.His139Tyr (c.415C>T)?

CD151 p.His139Tyr (c.415C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CD151 p.His139Tyr (c.415C>T) in the general population?

CD151 p.His139Tyr (c.415C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CD151 p.His139Tyr (c.415C>T)?

AlphaMissense predicts likely benign (score 0.1139) — an in-silico prediction, not a clinical call.

CD151 p.His139Tyr

c.415C>T · rs770842620 · VCV1908723

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1139 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1139	likely benign
REVEL	0.306	indeterminate
SaProt	LLR -5.85	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 2,119 bp · p 0.3 · regional, not allelic
Overall
CADD	17.38	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 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00103% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00083%

Overall 0.00136% 22/1,612,904 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
European (non-Finnish)	0.00161%	62,104
African / African-American	0.00133%	74,936
South Asian	0.0011%	91,080

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.His139Tyr
Coding: c.415C>T
MANE Select: NM_004357
dbSNP: rs770842620
Type: single nucleotide variant
Location: chr11:837313 (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.His139= Likely benign ★★ same residue
CD151 p.His139Leu Uncertain significance ★ ⚠ 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.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-his139tyr (accessed [today's date]).

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