Is ASPM p.Ala1804fs (c.5409del) pathogenic?

ASPM p.Ala1804fs (c.5409del) is classified Likely pathogenic in ASPM (ClinVar, Single submitter, 1 submitter; last evaluated 2020-01-21). Absent from gnomAD v4.1.

How common is ASPM p.Ala1804fs (c.5409del) in the general population?

ASPM p.Ala1804fs (c.5409del) is absent from gnomAD v4.1 (gnomAD).

ASPM p.Ala1804fs

c.5409del · rs1461653803 · VCV995272

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,930)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 18 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.9	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,930). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ASPM
Protein: p.Ala1804fs
Coding: c.5409del
MANE Select: NM_018136
dbSNP: rs1461653803
Type: Deletion
Location: chr1:197103842 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1804: the iq 8 domain

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

Similar variants

ASPM p.Ala3113fs Pathogenic ★★ same type
ASPM p.Arg2005fs Pathogenic ★★ same type
ASPM p.Asn1095fs Likely pathogenic ★★ same type
ASPM p.Asn3136fs Likely pathogenic ★★ same type
ASPM p.Asn324fs Pathogenic/Likely pathogenic ★★ same type
ASPM p.Asn394fs Pathogenic ★★ same type
ASPM p.Asp1285fs Pathogenic/Likely pathogenic ★★ same type
ASPM p.Asp990fs Pathogenic ★★ 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/aspm-p-ala1804fs (accessed [today's date]).

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