Is ITGAM p.Val643Met (c.1926_1927delinsAA) pathogenic?

ITGAM p.Val643Met (c.19261927delinsAA) is classified Uncertain significance in ITGAM (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-28). No gnomAD frequency available for this variant.

How common is ITGAM p.Val643Met (c.1926_1927delinsAA) in the general population?

ITGAM p.Val643Met (c.1926_1927delinsAA) is no gnomAD frequency available for this variant (gnomAD).

ITGAM p.Val643Met

c.1926_1927delinsAA · rs2144482866 · VCV1483645

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.1	GERP -2.2
Regional constraint	o/e 0.91	unconstrained · MANE · 72 kb · p 0.00026 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ITGAM
Protein: p.Val643Met
Coding: c.1926_1927delinsAA
MANE Select: NM_000632
dbSNP: rs2144482866
Type: Indel
Location: chr16:31321551 (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

Similar variants

ITGAM p.Val643Ala Uncertain significance ★ ⚠ same residue
ITGAM c.2709-15_2709-14delinsGC Uncertain significance ★ same type
ITGAM c.704+9_704+10delinsTG Uncertain significance ★ same type
ITGAM p.Ala152Ile Uncertain significance ★ same type
ITGAM p.Ala94Gly Uncertain significance ★ same type
ITGAM p.Gln101Pro Uncertain significance ★ same type
ITGAM p.Pro1147Leu 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-val643met (accessed [today's date]).

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