Is MAF p.Ser57Phe (c.170C>T) pathogenic?

MAF p.Ser57Phe (c.170C>T) is classified Likely pathogenic in MAF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-19). AlphaMissense: likely pathogenic (0.9987); No allele count reported in gnomAD v4.1 (AN 1,612,816); Associated with Inborn genetic diseases.

What condition is associated with MAF p.Ser57Phe (c.170C>T)?

MAF p.Ser57Phe (c.170C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MAF p.Ser57Phe (c.170C>T) in the general population?

MAF p.Ser57Phe (c.170C>T) is no allele count reported in gnomAD v4.1 (AN 1,612,816) (gnomAD).

What do computational predictors say about MAF p.Ser57Phe (c.170C>T)?

AlphaMissense predicts likely pathogenic (score 0.9987) — an in-silico prediction, not a clinical call.

MAF p.Ser57Phe

c.170C>T · rs1555530080 · VCV521242

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9987 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,816)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9987	likely pathogenic ✓ concordant with ClinVar · top 10% in MAF
REVEL	0.842	moderately pathogenic-leaning
SaProt	LLR -10.69	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9	GERP 2.4, phastCons 1
Regional constraint	o/e 0.25	constrained · MANE · 33 bp · p 0.0024 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,816). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAF
Protein: p.Ser57Phe
Coding: c.170C>T
MANE Select: NM_005360
dbSNP: rs1555530080
Type: single nucleotide variant
Location: chr16:79599733 (GRCh38)
Gene constraint: LOEUF 0.852 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.21
Residue 57: the 'disordered' region

Full MAF 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

MAF p.Arg306Gly Pathogenic/Likely pathogenic ★★ same condition
MAF p.His394Leu Uncertain significance ★★ same condition
WWOX p.Ala388Val Uncertain significance ★★ ⚠ same condition
WWOX p.Ala399Thr Uncertain significance ★★ ⚠ same condition
WWOX p.Arg395Trp Uncertain significance ★★ ⚠ same condition
WWOX p.Glu391Gly Uncertain significance ★★ ⚠ same condition
WWOX p.Glu402Gln Uncertain significance ★★ ⚠ same condition
WWOX p.Val360Met 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/maf-p-ser57phe (accessed [today's date]).

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