Is CD160 p.Glu71Gln (c.211G>C) pathogenic?

CD160 p.Glu71Gln (c.211G>C) is classified Uncertain significance in CD160 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-13). AlphaMissense: likely benign (0.1877); Ultra-rare (popmax 0.0165%, mid).

How common is CD160 p.Glu71Gln (c.211G>C) in the general population?

CD160 p.Glu71Gln (c.211G>C) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about CD160 p.Glu71Gln (c.211G>C)?

AlphaMissense predicts likely benign (score 0.1877) — an in-silico prediction, not a clinical call.

CD160 p.Glu71Gln

c.211G>C · VCV4650408

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1877 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1877	likely benign
SaProt	LLR -7.72	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 1.6	GERP 1.1, phastCons 0.95
Regional constraint	o/e 0.85	unconstrained · MANE · 10 kb · p 0.032 · regional, not allelic
Overall
CADD	19.07	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 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000547% 8/1,461,768 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
European (non-Finnish)	0.000593%	168,573

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.Glu71Gln
Coding: c.211G>C
MANE Select: NM_007053
Type: single nucleotide variant
Location: chr1:145730881 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 75.65 · 4 PDB
Residue 71: an α-helix; the ig-like v-type domain; a disulfide bond

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.Glu90Lys Uncertain significance ★ ⚠ same type
CD160 p.His106Arg 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-glu71gln (accessed [today's date]).

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