Is MACF1 p.Pro4534Ala (c.13600C>G) pathogenic?

MACF1 p.Pro4534Ala (c.13600C>G) is classified Uncertain significance in MACF1 (ClinVar, Single submitter, 1 submitter). AlphaMissense: likely benign (0.1799); Absent from gnomAD v4.1; Associated with lissencephaly 9 with complex brainstem malformation.

What condition is associated with MACF1 p.Pro4534Ala (c.13600C>G)?

MACF1 p.Pro4534Ala (c.13600C>G) is associated with lissencephaly 9 with complex brainstem malformation (ClinVar).

How common is MACF1 p.Pro4534Ala (c.13600C>G) in the general population?

MACF1 p.Pro4534Ala (c.13600C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MACF1 p.Pro4534Ala (c.13600C>G)?

AlphaMissense predicts likely benign (score 0.1799) — an in-silico prediction, not a clinical call.

MACF1 p.Pro4534Ala

c.13600C>G · rs867566442 · VCV2585381

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1799 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

lissencephaly 9 with complex brainstem malformation

Computational evidence

Protein change
AlphaMissense	0.1799	likely benign
REVEL	0.317	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6	GERP 2.3, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 93 kb · p 4.8e-14 · regional, not allelic
Overall
CADD	19.34	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P4539A vs ClinVar P4534A) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MACF1
Protein: p.Pro4534Ala
Coding: c.13600C>G
MANE Select: NM_001394062
dbSNP: rs867566442
Type: single nucleotide variant
Location: chr1:39380325 (GRCh38)
Gene constraint: LOEUF 0.238 · pLI 1.00 (gnomAD)

Full MACF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lissencephaly 9 with complex brainstem malformation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MACF1 p.Pro4534= Likely benign same residue
MACF1 p.Arg7251Pro Likely pathogenic ★★ same condition
MACF1 p.Arg30Gln Uncertain significance ★★ same condition
MACF1 p.Arg3713Cys Uncertain significance ★★ ⚠ same condition
MACF1 p.Arg6864Gln Uncertain significance ★★ same condition
MACF1 p.Arg7005Trp Uncertain significance ★★ ⚠ same condition
MACF1 p.Glu6915Lys Uncertain significance ★★ same condition
MACF1 p.Ile380Thr Uncertain significance ★★ ⚠ 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/macf1-p-pro4534ala (accessed [today's date]).

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