Is PRDM12 p.Phe271Val (c.811T>G) pathogenic?

PRDM12 p.Phe271Val (c.811T>G) is classified Likely pathogenic in PRDM12 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-05-23). AlphaMissense: likely pathogenic (0.9937); Absent from gnomAD v4.1.

How common is PRDM12 p.Phe271Val (c.811T>G) in the general population?

PRDM12 p.Phe271Val (c.811T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRDM12 p.Phe271Val (c.811T>G)?

AlphaMissense predicts likely pathogenic (score 0.9937) — an in-silico prediction, not a clinical call.

PRDM12 p.Phe271Val

c.811T>G · rs768643868 · VCV430206

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9937 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9937	likely pathogenic ✓ concordant with ClinVar · top 4% in PRDM12
REVEL	0.595	indeterminate
SaProt	LLR -15.58	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.4, phastCons 1
Regional constraint	o/e 1.53	unconstrained · MANE · 35 bp · p 0.024 · regional, not allelic
Overall
CADD	34.0	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: PRDM12
Protein: p.Phe271Val
Coding: c.811T>G
MANE Select: NM_021619
dbSNP: rs768643868
Type: single nucleotide variant
Location: chr9:130681376 (GRCh38)
Gene constraint: LOEUF 1.153 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.81 · 1 PDB

Full PRDM12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRDM12 p.Ala332Val Uncertain significance ★★ ⚠ same type
PRDM12 p.Arg147Cys Uncertain significance ★★ ⚠ same type
PRDM12 p.Arg147His Uncertain significance ★★ ⚠ same type
PRDM12 p.Arg158Trp Uncertain significance ★★ ⚠ same type
PRDM12 p.Asn134Ser Uncertain significance ★★ ⚠ same type
PRDM12 p.Asn141Ser Uncertain significance ★★ ⚠ same type
PRDM12 p.Asn207Ser Uncertain significance ★★ ⚠ same type
PRDM12 p.Asn277Lys 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/prdm12-p-phe271val (accessed [today's date]).

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