Is CD160 p.Gly84Arg (c.250G>A) pathogenic?

CD160 p.Gly84Arg (c.250G>A) is classified Benign in CD160 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-07-31). AlphaMissense: likely benign (0.1331); Rare (popmax 0.775%, nfe).

How common is CD160 p.Gly84Arg (c.250G>A) in the general population?

CD160 p.Gly84Arg (c.250G>A) is rare (popmax 0.775%, nfe) (gnomAD).

What do computational predictors say about CD160 p.Gly84Arg (c.250G>A)?

AlphaMissense predicts likely benign (score 0.1331) — an in-silico prediction, not a clinical call.

CD160 p.Gly84Arg

c.250G>A · rs148311134 · VCV718727

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1331 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.775%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.1331	likely benign
SaProt	LLR -6.46	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 2.6	GERP -0.89, phastCons 0.58
Regional constraint	o/e 0.85	unconstrained · MANE · 10 kb · p 0.032 · regional, not allelic
Overall
CADD	6.614	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.775% European (non-Finnish) · 9,146/1,179,994 alleles

Filtering AF 0.762% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.756%

Overall 0.647% 10,442/1,614,164 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	7.57%	13
Finnishnot grpmax-eligible	0.86%	116
European (non-Finnish)grpmax	0.775%	129
Remaining individualsnot grpmax-eligible	0.478%	209
Middle Eastern	0.198%	505
Admixed American	0.197%	509
South Asian	0.16%	624
African / African-American	0.0973%	1,028
Ashkenazi Jewishnot grpmax-eligible	0.0946%	1,057

Amish 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: CD160
Protein: p.Gly84Arg
Coding: c.250G>A
MANE Select: NM_007053
dbSNP: rs148311134
Type: single nucleotide variant
Location: chr1:145730920 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 75.65 · 4 PDB
Residue 84: 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.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
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-gly84arg (accessed [today's date]).

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