Is MAF p.Ala207Ser (c.619G>T) pathogenic?

MAF p.Ala207Ser (c.619G>T) is classified Likely benign in MAF (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-07). AlphaMissense: likely benign (0.0845); No allele count reported in gnomAD v4.1 (AN 979,204); Associated with Inborn genetic diseases.

What condition is associated with MAF p.Ala207Ser (c.619G>T)?

MAF p.Ala207Ser (c.619G>T) is associated with Inborn genetic diseases (ClinVar).

How common is MAF p.Ala207Ser (c.619G>T) in the general population?

MAF p.Ala207Ser (c.619G>T) is no allele count reported in gnomAD v4.1 (AN 979,204) (gnomAD).

What do computational predictors say about MAF p.Ala207Ser (c.619G>T)?

AlphaMissense predicts likely benign (score 0.0845) — an in-silico prediction, not a clinical call.

MAF p.Ala207Ser

c.619G>T · rs2143807424 · VCV2534263

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0845 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 979,204)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0845	likely benign
REVEL	0.3	indeterminate
SaProt	LLR -7.43	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.73	GERP -3, phastCons 0.45
Regional constraint	o/e 1.08	unconstrained · MANE · 679 bp · p 0.14 · regional, not allelic
Overall
CADD	5.742	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 979,204). 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.Ala207Ser
Coding: c.619G>T
MANE Select: NM_005360
dbSNP: rs2143807424
Type: single nucleotide variant
Location: chr16:79599284 (GRCh38)
Gene constraint: LOEUF 0.852 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.21
Residue 207: the 'represses are-mediated transcription' region; 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.Ala207= Likely benign ★ same residue
MAF p.Arg306Gly Pathogenic/Likely pathogenic ★★ same condition
MAF p.Ser57Phe 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

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-ala207ser (accessed [today's date]).

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