Is SCP2 p.Ala95Ser (c.283G>T) pathogenic?

SCP2 p.Ala95Ser (c.283G>T) is classified Likely benign in SCP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-22). AlphaMissense: likely benign (0.081); Absent from gnomAD v4.1.

How common is SCP2 p.Ala95Ser (c.283G>T) in the general population?

SCP2 p.Ala95Ser (c.283G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SCP2 p.Ala95Ser (c.283G>T)?

AlphaMissense predicts likely benign (score 0.081) — an in-silico prediction, not a clinical call.

SCP2 p.Ala95Ser

c.283G>T · VCV4581346

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.081 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.081	likely benign
REVEL	0.326	indeterminate
SaProt	LLR -3.86	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.62	GERP -3.8
Regional constraint	o/e 0.90	unconstrained · MANE · 112 kb · p 0.012 · regional, not allelic
Overall
CADD	7.288	PHRED · no single calibrated threshold — expert panels disagree

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: SCP2
Protein: p.Ala95Ser
Coding: c.283G>T
MANE Select: NM_002979
Type: single nucleotide variant
Location: chr1:52950838 (GRCh38)
Gene constraint: LOEUF 0.944 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.39 · 2 PDB

Full SCP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SCP2 p.Ala95Pro Uncertain significance ★ ⚠ same residue
SCP2 c.825+1G>T Pathogenic/Likely pathogenic ★★ same type
SCP2 p.Gln371Ter Pathogenic ★★ same type
SCP2 p.Ala359Val Uncertain significance ★★ ⚠ same type
SCP2 p.Ala427Gly Uncertain significance ★★ ⚠ same type
SCP2 p.Ala46Val Uncertain significance ★★ ⚠ same type
SCP2 p.Ala545Asp Uncertain significance ★★ same type
SCP2 p.Arg105Cys 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/scp2-p-ala95ser (accessed [today's date]).

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