Is MACF1 p.Ser1193Pro (c.3577T>C) pathogenic?

MACF1 p.Ser1193Pro (c.3577T>C) is classified Conflicting classifications of pathogenicity in MACF1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-02-16). AlphaMissense: likely benign (0.276); Ultra-rare (popmax 0.0133%, amr); Associated with Inborn genetic diseases.

What condition is associated with MACF1 p.Ser1193Pro (c.3577T>C)?

MACF1 p.Ser1193Pro (c.3577T>C) is associated with Inborn genetic diseases (ClinVar).

How common is MACF1 p.Ser1193Pro (c.3577T>C) in the general population?

MACF1 p.Ser1193Pro (c.3577T>C) is ultra-rare (popmax 0.0133%, amr) (gnomAD).

What do computational predictors say about MACF1 p.Ser1193Pro (c.3577T>C)?

AlphaMissense predicts likely benign (score 0.276) — an in-silico prediction, not a clinical call.

MACF1 p.Ser1193Pro

c.3577T>C · rs751454750 · VCV3121881

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.276 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.276	likely benign
REVEL	0.403	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 0.86, phastCons 0.89
Regional constraint	o/e 0.90	unconstrained · MANE · 39 kb · p 0.00039 · regional, not allelic
Overall
CADD	19.72	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 S1198P vs ClinVar S1193P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% Admixed American · 8/59,960 alleles

Filtering AF 0.00662% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00483%

Overall 0.00279% 45/1,613,338 alleles · ultra-rare exomes 36/1,461,110 · genomes 9/152,228 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0133%	7,495
European (non-Finnish)	0.00305%	32,767
Remaining individualsnot grpmax-eligible	0.0016%	62,456

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.Ser1193Pro
Coding: c.3577T>C
MANE Select: NM_001394062
dbSNP: rs751454750
Type: single nucleotide variant
Location: chr1:39316518 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MACF1 p.Ser1193Leu Likely benign ★ same residue
MACF1 p.Ala5598Ser Uncertain significance ★★ same condition
MACF1 p.Ala601Pro Uncertain significance ★★ ⚠ same condition
MACF1 p.Arg30Gln Uncertain significance ★★ same condition
MACF1 p.Arg3713Cys Uncertain significance ★★ ⚠ same condition
MACF1 p.Arg4674Cys Uncertain significance ★★ same condition
MACF1 p.Arg5490Gln Uncertain significance ★★ ⚠ same condition
MACF1 p.Arg5875Cys 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-ser1193pro (accessed [today's date]).

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