Is ITGAM p.Arg167= (c.501G>A) pathogenic?

ITGAM p.Arg167= (c.501G>A) is classified Likely benign in ITGAM (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-07). Very rare (popmax 0.00347%, sas).

How common is ITGAM p.Arg167= (c.501G>A) in the general population?

ITGAM p.Arg167= (c.501G>A) is very rare (popmax 0.00347%, sas) (gnomAD).

ITGAM p.Arg167=

c.501G>A · rs768385022 · VCV1570551

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00347%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.18	GERP -3.7
Overall
CADD	3.873	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00347% South Asian · 3/86,536 alleles

Filtering AF 0.000921% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000455%

Overall 0.000558% 8/1,433,072 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00347%	28,845
European (non-Finnish)	0.00043%	232,493

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.Arg167=
Coding: c.501G>A
MANE Select: NM_000632
dbSNP: rs768385022
Type: single nucleotide variant
Location: chr16:31271027 (GRCh38)
Gene constraint: LOEUF 0.678 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.30 · 31 PDB
Residue 167: the vwfa domain; an α-helix

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

Similar variants

ITGAM p.Arg167Gln Uncertain significance ★ ⚠ same residue
ITGAM p.Arg167Trp 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

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-arg167 (accessed [today's date]).

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