Is ITGAM p.Arg168Trp (c.502C>T) pathogenic?

ITGAM p.Arg168Trp (c.502C>T) is classified Uncertain significance in ITGAM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-13). AlphaMissense: likely benign (0.256); Ultra-rare (popmax 0.0128%, sas).

How common is ITGAM p.Arg168Trp (c.502C>T) in the general population?

ITGAM p.Arg168Trp (c.502C>T) is ultra-rare (popmax 0.0128%, sas) (gnomAD).

What do computational predictors say about ITGAM p.Arg168Trp (c.502C>T)?

AlphaMissense predicts likely benign (score 0.256) — an in-silico prediction, not a clinical call.

ITGAM p.Arg168Trp

c.502C>T · rs776216667 · VCV1389435

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.256 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0128%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.256	likely benign
REVEL	0.331	indeterminate
SaProt	LLR -11.60	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -3.4
Regional constraint	o/e 0.91	unconstrained · MANE · 72 kb · p 0.00026 · regional, not allelic
Overall
CADD	18.39	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 0.0128% South Asian · 11/86,232 alleles

Filtering AF 0.00712% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00548%

Overall 0.00183% 29/1,582,694 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0128%	7,839
Admixed American	0.00344%	29,093
African / African-American	0.00135%	74,012
European (non-Finnish)	0.00129%	77,425

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: ITGAM
Protein: p.Arg168Trp
Coding: c.502C>T
MANE Select: NM_000632
dbSNP: rs776216667
Type: single nucleotide variant
Location: chr16:31271028 (GRCh38)
Gene constraint: LOEUF 0.678 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.30 · 31 PDB
Residue 168: the vwfa domain; an α-helix

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

Similar variants

ITGAM p.Arg168Gln Uncertain significance ★ ⚠ same residue
ITGAM c.704+5G>A Uncertain significance ★★ same type
ITGAM p.Ala31Thr Uncertain significance ★★ ⚠ same type
ITGAM p.Ala433Val Uncertain significance ★★ ⚠ same type
ITGAM p.Ala753Val Uncertain significance ★★ ⚠ same type
ITGAM p.Ala943Val Uncertain significance ★★ ⚠ same type
ITGAM p.Arg1003His Uncertain significance ★★ ⚠ same type
ITGAM p.Arg131Trp 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/itgam-p-arg168trp (accessed [today's date]).

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