Is CD160 p.Phe151Tyr (c.452T>A) pathogenic?

CD160 p.Phe151Tyr (c.452T>A) is classified Uncertain significance in CD160 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-29). AlphaMissense: likely benign (0.1227); Ultra-rare (popmax 0.015%, amr).

How common is CD160 p.Phe151Tyr (c.452T>A) in the general population?

CD160 p.Phe151Tyr (c.452T>A) is ultra-rare (popmax 0.015%, amr) (gnomAD).

What do computational predictors say about CD160 p.Phe151Tyr (c.452T>A)?

AlphaMissense predicts likely benign (score 0.1227) — an in-silico prediction, not a clinical call.

CD160 p.Phe151Tyr

c.452T>A · rs879994994 · VCV2593395

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1227 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.015%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1227	likely benign
SaProt	LLR -6.38	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.37	GERP -1.8
Regional constraint	o/e 0.85	unconstrained · MANE · 10 kb · p 0.032 · regional, not allelic
Overall
CADD	7.287	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; SaProt is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.015% Admixed American · 9/60,002 alleles

Filtering AF 0.00773% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00579%

Overall 0.00112% 18/1,613,898 alleles · ultra-rare exomes 6/1,461,710 · genomes 12/152,188 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.015%	6,667
Remaining individualsnot grpmax-eligible	0.008%	12,496
African / African-American	0.00534%	18,730

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: CD160
Protein: p.Phe151Tyr
Coding: c.452T>A
MANE Select: NM_007053
dbSNP: rs879994994
Type: single nucleotide variant
Location: chr1:145736048 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 75.65 · 4 PDB

Full CD160 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD160 p.Gly84Arg Benign ★★ same type
CD160 p.Arg122Cys Uncertain significance ★ ⚠ same type
CD160 p.Gln101His Uncertain significance ★ ⚠ same type
CD160 p.Gln117Arg Uncertain significance ★ ⚠ same type
CD160 p.Gln164Pro Uncertain significance ★ ⚠ same type
CD160 p.Glu54Asp Uncertain significance ★ ⚠ same type
CD160 p.Glu71Gln Uncertain significance ★ ⚠ same type
CD160 p.Glu90Lys 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/cd160-p-phe151tyr (accessed [today's date]).

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