Is CLASP2 p.Asp1262= (c.3786C>T) pathogenic?

CLASP2 p.Asp1262= (c.3786C>T) is classified Likely benign in CLASP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-10). Rare (popmax 0.107%, eas); Associated with CLASP2-related disorder.

What condition is associated with CLASP2 p.Asp1262= (c.3786C>T)?

CLASP2 p.Asp1262= (c.3786C>T) is associated with CLASP2-related disorder (ClinVar).

How common is CLASP2 p.Asp1262= (c.3786C>T) in the general population?

CLASP2 p.Asp1262= (c.3786C>T) is rare (popmax 0.107%, eas) (gnomAD).

CLASP2 p.Asp1262=

c.3786C>T · rs551664425 · VCV3050390

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.107%, eas)

Conditions

CLASP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -4.8
Overall
CADD	7.261	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.107% East Asian · 48/44,858 alleles

Filtering AF 0.0829% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0743%

Overall 0.00385% 62/1,609,598 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.107%	935
Admixed American	0.005%	19,995
South Asian	0.0033%	30,305
Remaining individualsnot grpmax-eligible	0.0016%	62,316
Finnishnot grpmax-eligible	0.00156%	64,004
European (non-Finnish)	0.00051%	196,006

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: CLASP2
Protein: p.Asp1262=
Coding: c.3786C>T
MANE Select: NM_001365631
dbSNP: rs551664425
Type: single nucleotide variant
Location: chr3:33535234 (GRCh38)
Gene constraint: LOEUF 0.365 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.98 · 7 PDB
Residue 1262: the 'interaction with rsn and localization to the golgi and kinetochores' region; the 'required for cortical localization' region

Full CLASP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CLASP2-related disorder

Similar variants

CLASP2 c.2240-4C>G Uncertain significance same condition
CLASP2 c.1694+8C>T Likely benign same condition
CLASP2 c.2455-1147C>G Benign same condition
CLASP2 p.Ala1461= Benign same condition
CLASP2 p.Asn872= Likely benign same condition
CLASP2 p.Asp1442= Likely benign same condition
CLASP2 p.Glu2= Likely benign same condition
CLASP2 p.Gly1192= Likely benign 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/clasp2-p-asp1262 (accessed [today's date]).

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