Is ASPM p.Ala663Ser (c.1987G>T) pathogenic?

ASPM p.Ala663Ser (c.1987G>T) is classified Benign/Likely benign in ASPM (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-18). AlphaMissense: likely benign (0.2169); Low-frequency (popmax 2.16%, afr); Associated with microcephaly 5, primary, autosomal recessive.

What condition is associated with ASPM p.Ala663Ser (c.1987G>T)?

ASPM p.Ala663Ser (c.1987G>T) is associated with microcephaly 5, primary, autosomal recessive (ClinVar).

How common is ASPM p.Ala663Ser (c.1987G>T) in the general population?

ASPM p.Ala663Ser (c.1987G>T) is low-frequency (popmax 2.16%, afr) (gnomAD).

What do computational predictors say about ASPM p.Ala663Ser (c.1987G>T)?

AlphaMissense predicts likely benign (score 0.2169) — an in-silico prediction, not a clinical call.

ASPM p.Ala663Ser

c.1987G>T · rs113611857 · VCV157790

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.2169 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.16%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

microcephaly 5, primary, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.2169	likely benign
REVEL	0.116	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 59 kb · p 0.59 · regional, not allelic
Overall
CADD	22.1	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.16% African / African-American · 1,619/74,936 alleles

Filtering AF 2.07% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.04%

Overall 0.118% 1,900/1,612,032 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.16%	46
Admixed American	0.178%	561
Remaining individualsnot grpmax-eligible	0.171%	583
Middle Eastern	0.0661%	1,513
South Asian	0.0121%	8,275
European (non-Finnish)	0.00441%	22,659

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.Ala663Ser
Coding: c.1987G>T
MANE Select: NM_018136
dbSNP: rs113611857
Type: single nucleotide variant
Location: chr1:197139806 (GRCh38)
Gene constraint: LOEUF 0.766 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

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.Ala663= Likely benign ★★ same residue
ASPM p.Ala663Val Uncertain significance ★ ⚠ 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-ala663ser (accessed [today's date]).

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