Is SAMD9 p.Arg106= (c.318T>C) pathogenic?

SAMD9 p.Arg106= (c.318T>C) is classified Likely benign in SAMD9 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-25). Very rare (popmax 0.00167%, amr); Associated with Inborn genetic diseases.

What condition is associated with SAMD9 p.Arg106= (c.318T>C)?

SAMD9 p.Arg106= (c.318T>C) is associated with Inborn genetic diseases (ClinVar).

How common is SAMD9 p.Arg106= (c.318T>C) in the general population?

SAMD9 p.Arg106= (c.318T>C) is very rare (popmax 0.00167%, amr) (gnomAD).

SAMD9 p.Arg106=

c.318T>C · VCV4824689

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Inborn genetic diseases

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 -1.3	GERP -2
Overall
CADD	1.751	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,010 alleles

Overall 0.000186% 3/1,614,054 alleles · very rare exomes 3/1,461,812 · genomes 0/152,242 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	60,010
Remaining individualsnot grpmax-eligible	0.0016%	62,504
European (non-Finnish)	8.47e-05%	1,180,006

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: SAMD9
Protein: p.Arg106=
Coding: c.318T>C
MANE Select: NM_017654
Type: single nucleotide variant
Location: chr7:93105780 (GRCh38)
Gene constraint: LOEUF 1.773 · pLI 0.03 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 83.79 · 10 PDB
Residue 106: the 'disordered' region

Full SAMD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SAMD9 p.Arg106Ser Likely benign ★ same residue
SAMD9 p.Arg106Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
SAMD9 p.Arg106His Likely benign ★ same residue
SAMD9 p.Ala1057Val Uncertain significance ★★ ⚠ same condition
SAMD9 p.Ala1066Thr Uncertain significance ★★ ⚠ same condition
SAMD9 p.Ala1069Thr Uncertain significance ★★ ⚠ same condition
SAMD9 p.Ala1082Gly Uncertain significance ★★ ⚠ same condition
SAMD9 p.Ala1102Asp Uncertain significance ★★ ⚠ same condition

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/samd9-p-arg106 (accessed [today's date]).

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