Is MACF1 p.Arg6827= (c.20479C>A) pathogenic?

MACF1 p.Arg6827= (c.20479C>A) is classified Benign in MACF1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-30). Common (popmax 9.75%, afr) — too common for a highly-penetrant pathogenic allele; Associated with lissencephaly 9 with complex brainstem malformation.

What condition is associated with MACF1 p.Arg6827= (c.20479C>A)?

MACF1 p.Arg6827= (c.20479C>A) is associated with lissencephaly 9 with complex brainstem malformation (ClinVar).

MACF1 p.Arg6827=

Q: How common is MACF1 p.Arg6827= (c.20479C>A) in the general population?

MACF1 p.Arg6827= (c.20479C>A) is common (popmax 9.75%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.20479C>A · rs1746838 · VCV1259495

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 9.75%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

lissencephaly 9 with complex brainstem malformation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.117	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 0.9, phastCons 1
Overall
CADD	9.075	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.75% African / African-American · 7,314/74,996 alleles

Filtering AF 9.57% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.49%

Overall 4.45% 71,868/1,613,990 alleles · common exomes 63,409/1,461,790 · genomes 8,459/152,200 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	9.75%	10
Amishnot grpmax-eligible	8.02%	12
South Asian	5.62%	18
European (non-Finnish)	4.35%	23
Finnishnot grpmax-eligible	4.19%	24
Remaining individualsnot grpmax-eligible	4.16%	24
Admixed American	2.9%	34
Ashkenazi Jewishnot grpmax-eligible	2.74%	37
Middle Eastern	2.62%	38
East Asian	0.0223%	4,488

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: MACF1
Protein: p.Arg6827=
Coding: c.20479C>A
MANE Select: NM_001394062
dbSNP: rs1746838
Type: single nucleotide variant
Location: chr1:39452216 (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.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
MACF1 p.Leu6865Phe 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-arg6827 (accessed [today's date]).

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