Is MAF p.Ser80= (c.240G>C) pathogenic?

MAF p.Ser80= (c.240G>C) is classified Likely benign in MAF (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-01-08). Low-frequency (popmax 1.26%, eas); Associated with MAF-related disorder.

What condition is associated with MAF p.Ser80= (c.240G>C)?

MAF p.Ser80= (c.240G>C) is associated with MAF-related disorder (ClinVar).

How common is MAF p.Ser80= (c.240G>C) in the general population?

MAF p.Ser80= (c.240G>C) is low-frequency (popmax 1.26%, eas) (gnomAD).

MAF p.Ser80=

c.240G>C · rs186864493 · VCV3058270

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.26%, eas)

Conditions

MAF-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP -0.008, phastCons 1
Overall
CADD	13.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.26% East Asian · 562/44,780 alleles

Filtering AF 1.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.14%

Overall 0.0355% 573/1,612,114 alleles · low-frequency exomes 551/1,459,908 · genomes 22/152,206 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	1.26%	80
Remaining individualsnot grpmax-eligible	0.00961%	10,404
European (non-Finnish)	0.000424%	235,924

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: MAF
Protein: p.Ser80=
Coding: c.240G>C
MANE Select: NM_005360
dbSNP: rs186864493
Type: single nucleotide variant
Location: chr16:79599663 (GRCh38)
Gene constraint: LOEUF 0.852 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.21
Residue 80: the 'disordered' region

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

Disease context

MAF-related disorder

Similar variants

MAF p.Ser54Trp Likely pathogenic ★ same condition
MAF c.1119-2A>G Uncertain significance ★ same condition
MAF p.Arg288Gly Uncertain significance ⚠ same condition
MAF p.Arg299Gly Uncertain significance ⚠ same condition
MAF p.Asp24Glu Uncertain significance ⚠ same condition
MAF p.Cys305Trp Uncertain significance ⚠ same condition
MAF p.Pro200Thr Uncertain significance ⚠ same condition
MAF p.Ala161= Likely benign 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/maf-p-ser80 (accessed [today's date]).

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