Is BSCL2 p.Arg270= (c.810C>T) pathogenic?

BSCL2 p.Arg270= (c.810C>T) is classified Conflicting classifications of pathogenicity in BSCL2 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-07-02). Ultra-rare (popmax 0.0825%, mid); Associated with Inborn genetic diseases.

What condition is associated with BSCL2 p.Arg270= (c.810C>T)?

BSCL2 p.Arg270= (c.810C>T) is associated with Inborn genetic diseases, congenital generalized lipodystrophy type 2, neuronopathy, distal hereditary motor, type 5A (ClinVar).

How common is BSCL2 p.Arg270= (c.810C>T) in the general population?

BSCL2 p.Arg270= (c.810C>T) is ultra-rare (popmax 0.0825%, mid) (gnomAD).

BSCL2 p.Arg270=

c.810C>T · rs998498207 · VCV515141

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0825%, mid)

Conditions

Inborn genetic diseases

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 0.14	GERP -3.3, phastCons 0.001
Overall
CADD	7.402	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0825% Middle Eastern · 5/6,060 alleles

Filtering AF 0.0324% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.021%

Overall 0.000547% 8/1,461,834 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0825%	1,212
European (non-Finnish)	0.000254%	393,345

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: BSCL2
Protein: p.Arg270=
Coding: c.810C>T
dbSNP: rs998498207
Type: single nucleotide variant
Location: chr11:62692429 (GRCh38)

Full BSCL2 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

Also linked: congenital generalized lipodystrophy type 2 neuronopathy, distal hereditary motor, type 5A Charcot-Marie-Tooth disease type 2

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/bscl2-p-arg270 (accessed [today's date]).

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