Is SAMD9 p.Ser336= (c.1008T>C) pathogenic?

SAMD9 p.Ser336= (c.1008T>C) is classified Likely benign in SAMD9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-01). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SAMD9 p.Ser336= (c.1008T>C)?

SAMD9 p.Ser336= (c.1008T>C) is associated with Inborn genetic diseases (ClinVar).

How common is SAMD9 p.Ser336= (c.1008T>C) in the general population?

SAMD9 p.Ser336= (c.1008T>C) is absent from gnomAD v4.1 (gnomAD).

SAMD9 p.Ser336=

c.1008T>C · VCV4159206

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.16	GERP -2.4
Overall
CADD	3.488	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SAMD9
Protein: p.Ser336=
Coding: c.1008T>C
MANE Select: NM_017654
Type: single nucleotide variant
Location: chr7:93105090 (GRCh38)
Gene constraint: LOEUF 1.773 · pLI 0.03 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 83.79 · 10 PDB

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.Ser336Gly Uncertain significance ★★ ⚠ same residue
SAMD9 p.Ser336Arg Uncertain significance ★ ⚠ same residue
SAMD9 p.Ser336Thr Uncertain significance ★ ⚠ same residue
SAMD9 p.Ser336Asn Uncertain significance ★ ⚠ 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

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-ser336 (accessed [today's date]).

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