Is SUN2 p.Pro580= (c.1740C>T) pathogenic?

SUN2 p.Pro580= (c.1740C>T) is classified Benign in SUN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-21). Rare (popmax 0.633%, sas); Associated with Emery-Dreifuss muscular dystrophy.

What condition is associated with SUN2 p.Pro580= (c.1740C>T)?

SUN2 p.Pro580= (c.1740C>T) is associated with Emery-Dreifuss muscular dystrophy (ClinVar).

How common is SUN2 p.Pro580= (c.1740C>T) in the general population?

SUN2 p.Pro580= (c.1740C>T) is rare (popmax 0.633%, sas) (gnomAD).

How is Emery-Dreifuss muscular dystrophy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SUN2 p.Pro580=

c.1740C>T · rs570193292 · VCV771679

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.633%, sas)

Conditions

Emery-Dreifuss muscular dystrophy

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.2	GERP -5.1
Overall
CADD	9.266	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.633% South Asian · 575/90,890 alleles

Filtering AF 0.59% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.573%

Overall 0.0373% 602/1,612,226 alleles · rare exomes 570/1,459,936 · genomes 32/152,290 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.633%	158
Remaining individualsnot grpmax-eligible	0.0337%	2,971
African / African-American	0.00267%	37,504
East Asian	0.00223%	44,844
Admixed American	0.00167%	59,874
European (non-Finnish)	0.00017%	589,442

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: SUN2
Protein: p.Pro580=
Coding: c.1740C>T
MANE Select: NM_015374
dbSNP: rs570193292
Type: single nucleotide variant
Location: chr22:38738912 (GRCh38)

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

Disease context

Emery-Dreifuss muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Emery-Dreifuss muscular dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

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-pro580 (accessed [today's date]).

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