Is ASPM p.Arg1019Ter (c.3055C>T) pathogenic?

ASPM p.Arg1019Ter (c.3055C>T) is classified Pathogenic in ASPM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-02-03). Very rare (popmax 0.0011%, nfe); Associated with ASPM-related disorder.

What condition is associated with ASPM p.Arg1019Ter (c.3055C>T)?

ASPM p.Arg1019Ter (c.3055C>T) is associated with ASPM-related disorder, microcephaly 5, primary, autosomal recessive (ClinVar).

How common is ASPM p.Arg1019Ter (c.3055C>T) in the general population?

ASPM p.Arg1019Ter (c.3055C>T) is very rare (popmax 0.0011%, nfe) (gnomAD).

ASPM p.Arg1019Ter

c.3055C>T · rs199422153 · VCV21571

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, nfe)

Conditions

ASPM-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 11 of 28
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.3	GERP 1, phastCons 0.89
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% European (non-Finnish) · 13/1,179,874 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.000889% 13/1,461,688 alleles · very rare

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: ASPM
Protein: p.Arg1019Ter
Coding: c.3055C>T
MANE Select: NM_018136
dbSNP: rs199422153
Type: single nucleotide variant
Location: chr1:197125073 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1019: the calponin-homology (ch) 1 domain

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

Disease context

ASPM-related disorder

Also linked: microcephaly 5, primary, autosomal recessive

Similar variants

ASPM p.Arg1019Leu Uncertain significance ★★ ⚠ same residue
ASPM p.Arg1019Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
ASPM c.2419+2T>C Pathogenic/Likely pathogenic ★★ same condition
ASPM c.2488-1G>C Pathogenic/Likely pathogenic ★★ same condition
ASPM c.2936+5G>A Likely pathogenic ★★ same condition
ASPM c.3082+1G>C Pathogenic/Likely pathogenic ★★ same condition
ASPM c.9084+5G>A Likely pathogenic ★★ same condition
ASPM p.Arg1271Ter Pathogenic ★★ 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/aspm-p-arg1019ter (accessed [today's date]).

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