Is SUN2 p.Asp372Ala (c.1115A>C) pathogenic?

SUN2 p.Asp372Ala (c.1115A>C) is classified Likely benign in SUN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-31). AlphaMissense: likely benign (0.1068); Absent from gnomAD v4.1.

How common is SUN2 p.Asp372Ala (c.1115A>C) in the general population?

SUN2 p.Asp372Ala (c.1115A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SUN2 p.Asp372Ala (c.1115A>C)?

AlphaMissense predicts likely benign (score 0.1068) — an in-silico prediction, not a clinical call.

SUN2 p.Asp372Ala

c.1115A>C · VCV4684490

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1068 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.1068	likely benign
REVEL	0.046	moderately benign-leaning
SaProt	LLR -5.21	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5	GERP 2.1, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 12 kb · p 0.11 · regional, not allelic
Overall
CADD	21.5	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: SUN2
Protein: p.Asp372Ala
Coding: c.1115A>C
MANE Select: NM_015374
Type: single nucleotide variant
Location: chr22:38741525 (GRCh38)

Full SUN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/sun2-p-asp372ala (accessed [today's date]).

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