Is PRDM7 p.Ala313Pro (c.937G>C) pathogenic?

PRDM7 p.Ala313Pro (c.937G>C) is classified Uncertain significance in PRDM7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-28). AlphaMissense: likely pathogenic (0.677); Absent from gnomAD v4.1.

How common is PRDM7 p.Ala313Pro (c.937G>C) in the general population?

PRDM7 p.Ala313Pro (c.937G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRDM7 p.Ala313Pro (c.937G>C)?

AlphaMissense predicts likely pathogenic (score 0.677) — an in-silico prediction, not a clinical call.

PRDM7 p.Ala313Pro

c.937G>C · VCV4571852

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.677 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.677	likely pathogenic · top 3% in PRDM7
REVEL	0.136	moderately benign-leaning
SaProt	LLR -12.06	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	phastCons 0.59
Regional constraint	o/e 0.96	unconstrained · MANE · 18 kb · p 0.35 · regional, not allelic
Overall
CADD	22.0	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: PRDM7
Protein: p.Ala313Pro
Coding: c.937G>C
MANE Select: NM_001098173
Type: single nucleotide variant
Location: chr16:90061465 (GRCh38)
Gene constraint: LOEUF 1.002 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.59
Residue 313: the set domain

Full PRDM7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRDM7 p.Ala122Val Uncertain significance ★ ⚠ same type
PRDM7 p.Ala264Val Uncertain significance ★ ⚠ same type
PRDM7 p.Ala322Asp Uncertain significance ★ ⚠ same type
PRDM7 p.Ala68Gly Uncertain significance ★ ⚠ same type
PRDM7 p.Arg237Cys Uncertain significance ★ ⚠ same type
PRDM7 p.Arg323Gln Uncertain significance ★ ⚠ same type
PRDM7 p.Arg323Trp Uncertain significance ★ ⚠ same type
PRDM7 p.Arg50His Uncertain significance ★ ⚠ 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/prdm7-p-ala313pro (accessed [today's date]).

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