Is SAMD9L p.Ser462Arg (c.1386T>A) pathogenic?

SAMD9L p.Ser462Arg (c.1386T>A) is classified Uncertain significance in SAMD9L (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-17). AlphaMissense: likely benign (0.2853); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SAMD9L p.Ser462Arg (c.1386T>A)?

SAMD9L p.Ser462Arg (c.1386T>A) is associated with Inborn genetic diseases (ClinVar).

How common is SAMD9L p.Ser462Arg (c.1386T>A) in the general population?

SAMD9L p.Ser462Arg (c.1386T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SAMD9L p.Ser462Arg (c.1386T>A)?

AlphaMissense predicts likely benign (score 0.2853) — an in-silico prediction, not a clinical call.

SAMD9L p.Ser462Arg

c.1386T>A · VCV3949929

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2853 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2853	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -5.15	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.31	phastCons 0.95
Regional constraint	o/e 0.84	unconstrained · MANE · 1,885 bp · p 3.1e-05 · regional, not allelic
Overall
CADD	13.55	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: SAMD9L
Protein: p.Ser462Arg
Coding: c.1386T>A
MANE Select: NM_152703
Type: single nucleotide variant
Location: chr7:93134586 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.85

Full SAMD9L 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

SAMD9L p.Ser462Thr Uncertain significance ★★ ⚠ same residue
SAMD9L p.Ser462Cys Uncertain significance ★ ⚠ same residue
SAMD9L p.Ser462Ile Uncertain significance ★ ⚠ same residue
SAMD9L p.Ala1073Thr Uncertain significance ★★ ⚠ same condition
SAMD9L p.Ala1087Asp Uncertain significance ★★ ⚠ same condition
SAMD9L p.Ala1106Thr Uncertain significance ★★ ⚠ same condition
SAMD9L p.Ala1106Val Uncertain significance ★★ ⚠ same condition
SAMD9L p.Ala1109Pro 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/samd9l-p-ser462arg (accessed [today's date]).

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