Is MACF1 p.Ser975Phe (c.2924C>T) pathogenic?

MACF1 p.Ser975Phe (c.2924C>T) is classified Conflicting classifications of pathogenicity in MACF1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-10-23). AlphaMissense: likely benign (0.1192); Ultra-rare (popmax 0.0239%, amr); Associated with Inborn genetic diseases.

What condition is associated with MACF1 p.Ser975Phe (c.2924C>T)?

MACF1 p.Ser975Phe (c.2924C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MACF1 p.Ser975Phe (c.2924C>T) in the general population?

MACF1 p.Ser975Phe (c.2924C>T) is ultra-rare (popmax 0.0239%, amr) (gnomAD).

What do computational predictors say about MACF1 p.Ser975Phe (c.2924C>T)?

AlphaMissense predicts likely benign (score 0.1192) — an in-silico prediction, not a clinical call.

MACF1 p.Ser975Phe

c.2924C>T · rs577233378 · VCV1690738

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1192 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0239%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1192	likely benign
REVEL	0.405	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP 1, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 39 kb · p 0.00039 · regional, not allelic
Overall
CADD	18.92	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 S980F vs ClinVar S975F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0239% Admixed American · 14/58,528 alleles

Filtering AF 0.0144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0115%

Overall 0.0018% 29/1,608,866 alleles · ultra-rare exomes 16/1,456,566 · genomes 13/152,300 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0239%	4,181
Remaining individualsnot grpmax-eligible	0.00963%	10,385
African / African-American	0.00669%	14,952
European (non-Finnish)	0.000339%	294,603

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.Ser975Phe
Coding: c.2924C>T
MANE Select: NM_001394062
dbSNP: rs577233378
Type: single nucleotide variant
Location: chr1:39310252 (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.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
MACF1 p.Arg6864Gln 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-ser975phe (accessed [today's date]).

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