Is CD160 p.His106Arg (c.317A>G) pathogenic?

CD160 p.His106Arg (c.317A>G) is classified Uncertain significance in CD160 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-04). AlphaMissense: likely benign (0.2058); Very rare (popmax 0.005%, nfe).

How common is CD160 p.His106Arg (c.317A>G) in the general population?

CD160 p.His106Arg (c.317A>G) is very rare (popmax 0.005%, nfe) (gnomAD).

What do computational predictors say about CD160 p.His106Arg (c.317A>G)?

AlphaMissense predicts likely benign (score 0.2058) — an in-silico prediction, not a clinical call.

CD160 p.His106Arg

c.317A>G · rs145560737 · VCV2412299

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2058 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.2058	likely benign
SaProt	LLR -7.20	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 -0.55, phastCons 0.87
Regional constraint	o/e 0.85	unconstrained · MANE · 10 kb · p 0.032 · regional, not allelic
Overall
CADD	11.51	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 0.005% European (non-Finnish) · 59/1,180,028 alleles

Filtering AF 0.00394% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00361%

Overall 0.00378% 61/1,614,078 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.005%	20,000
Remaining individualsnot grpmax-eligible	0.0032%	31,243

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.His106Arg
Coding: c.317A>G
MANE Select: NM_007053
dbSNP: rs145560737
Type: single nucleotide variant
Location: chr1:145730987 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 75.65 · 4 PDB
Residue 106: 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.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-his106arg (accessed [today's date]).

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