Is ASPM p.Arg1405Pro (c.4214G>C) pathogenic?

ASPM p.Arg1405Pro (c.4214G>C) is classified Uncertain significance in ASPM (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-22). AlphaMissense: likely pathogenic (0.6482); Very rare (popmax 0.00535%, afr); Associated with microcephaly 5, primary, autosomal recessive.

What condition is associated with ASPM p.Arg1405Pro (c.4214G>C)?

ASPM p.Arg1405Pro (c.4214G>C) is associated with microcephaly 5, primary, autosomal recessive (ClinVar).

How common is ASPM p.Arg1405Pro (c.4214G>C) in the general population?

ASPM p.Arg1405Pro (c.4214G>C) is very rare (popmax 0.00535%, afr) (gnomAD).

What do computational predictors say about ASPM p.Arg1405Pro (c.4214G>C)?

AlphaMissense predicts likely pathogenic (score 0.6482) — an in-silico prediction, not a clinical call.

ASPM p.Arg1405Pro

c.4214G>C · rs143092798 · VCV294631

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6482 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00535%, afr)

Missense predictors

2/2 damaging

AlphaMissense, REVEL

Conditions

microcephaly 5, primary, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.6482	likely pathogenic · top 9% in ASPM
REVEL	0.779	moderately pathogenic-leaning
⇒ AlphaMissense and REVEL both call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.038	GERP 1.4, phastCons 0.001
Regional constraint	o/e 1.01	unconstrained · MANE · 59 kb · p 0.59 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00535% African / African-American · 4/74,704 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000311% 5/1,610,242 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00535%	18,676
Admixed American	0.00168%	59,690

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.Arg1405Pro
Coding: c.4214G>C
MANE Select: NM_018136
dbSNP: rs143092798
Type: single nucleotide variant
Location: chr1:197105037 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1405: the iq 2 domain

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

Disease context

microcephaly 5, primary, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ASPM p.Arg1405His Uncertain significance ★★ ⚠ same residue
ASPM p.Arg1405Cys Benign/Likely benign ★★ ⚠ 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.Arg1019Ter 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-arg1405pro (accessed [today's date]).

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