Is ITGAM p.Ser344= (c.1032C>T) pathogenic?

ITGAM p.Ser344= (c.1032C>T) is classified Likely benign in ITGAM (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-06-20). Very rare (popmax 0.00442%, sas); Associated with ITGAM-related disorder.

What condition is associated with ITGAM p.Ser344= (c.1032C>T)?

ITGAM p.Ser344= (c.1032C>T) is associated with ITGAM-related disorder (ClinVar).

How common is ITGAM p.Ser344= (c.1032C>T) in the general population?

ITGAM p.Ser344= (c.1032C>T) is very rare (popmax 0.00442%, sas) (gnomAD).

ITGAM p.Ser344=

c.1032C>T · rs778809073 · VCV3050736

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00442%, sas)

Conditions

ITGAM-related disorder

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 -0.003	GERP -1.9, phastCons 0.66
Overall
CADD	10.23	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00442% South Asian · 4/90,560 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000895%

Overall 0.000372% 6/1,611,932 alleles · very rare exomes 6/1,459,728 · genomes 0/152,204 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00442%	22,640
European (non-Finnish)	0.00017%	589,473

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.Ser344=
Coding: c.1032C>T
MANE Select: NM_000632
dbSNP: rs778809073
Type: single nucleotide variant
Location: chr16:31276693 (GRCh38)
Gene constraint: LOEUF 0.678 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.30 · 31 PDB

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

Disease context

ITGAM-related disorder

Similar variants

ITGAM p.Ser344Arg Uncertain significance ★★ ⚠ same residue
ITGAM p.Ser344Asn Uncertain significance ★ ⚠ same residue
ITGAM c.704+5G>A Uncertain significance ★★ same condition
ITGAM p.Arg579Ser Uncertain significance ★★ ⚠ same condition
ITGAM p.Pro750Ala Uncertain significance ★ ⚠ same condition
ITGAM p.Pro265= Likely benign same condition
ITGAM p.Ala31Thr Uncertain significance ★★ ⚠ same type
ITGAM p.Ala433Val 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-ser344 (accessed [today's date]).

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