Is MAF p.Lys320Arg (c.959A>G) pathogenic?

MAF p.Lys320Arg (c.959A>G) is classified Uncertain significance in MAF (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-14). AlphaMissense: ambiguous (0.5156); Absent from gnomAD v4.1.

How common is MAF p.Lys320Arg (c.959A>G) in the general population?

MAF p.Lys320Arg (c.959A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAF p.Lys320Arg (c.959A>G)?

AlphaMissense predicts ambiguous (score 0.5156) — an in-silico prediction, not a clinical call.

MAF p.Lys320Arg

c.959A>G · rs2507654121 · VCV2444704

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5156 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.5156	ambiguous
REVEL	0.748	pathogenic-leaning
SaProt	LLR -9.73	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 0.093, phastCons 1
Regional constraint	o/e 1.14	unconstrained · MANE · 4,496 bp · p 0.15 · 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MAF
Protein: p.Lys320Arg
Coding: c.959A>G
MANE Select: NM_005360
dbSNP: rs2507654121
Type: single nucleotide variant
Location: chr16:79598944 (GRCh38)
Gene constraint: LOEUF 0.852 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.21
Residue 320: the bzip domain; a UniProt-annotated variant site (in ctrct21); the 'represses are-mediated transcription' region; the 'leucine-zipper' region

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

Similar variants

MAF p.Ala302Val Pathogenic/Likely pathogenic ★★ same type
MAF p.Arg299Cys Pathogenic/Likely pathogenic ★★ same type
MAF p.Arg306Gly Pathogenic/Likely pathogenic ★★ same type
MAF p.Cys305Phe Likely pathogenic ★★ same type
MAF p.Pro59His Pathogenic/Likely pathogenic ★★ same type
MAF p.Ser54Leu Pathogenic ★★ same type
MAF p.Ser57Phe Likely pathogenic ★★ same type
MAF p.Ser66Leu Pathogenic ★★ same type

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-lys320arg (accessed [today's date]).

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