Is POMP p.Pro76Thr (c.226C>A) pathogenic?

POMP p.Pro76Thr (c.226C>A) is classified Uncertain significance in POMP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-01). AlphaMissense: likely pathogenic (0.7938); Absent from gnomAD v4.1.

How common is POMP p.Pro76Thr (c.226C>A) in the general population?

POMP p.Pro76Thr (c.226C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about POMP p.Pro76Thr (c.226C>A)?

AlphaMissense predicts likely pathogenic (score 0.7938) — an in-silico prediction, not a clinical call.

POMP p.Pro76Thr

c.226C>A · rs772222545 · VCV1505681

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7938 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7938	likely pathogenic
REVEL	0.685	pathogenic-leaning
SaProt	LLR -14.88	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 7.6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 19 kb · p 0.048 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: POMP
Protein: p.Pro76Thr
Coding: c.226C>A
MANE Select: NM_015932
dbSNP: rs772222545
Type: single nucleotide variant
Location: chr13:28668536 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 81.76 · 11 PDB
Residue 76: an α-helix

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

Similar variants

POMP p.Pro76Leu Uncertain significance ★★ ⚠ same residue
POMP p.Pro76Ser Uncertain significance ★★ ⚠ same residue
POMP p.Pro76= Likely benign ★★ same residue
POMP p.Arg32Gln Uncertain significance ★★ ⚠ same type
POMP p.Arg32Trp Uncertain significance ★★ ⚠ same type
POMP p.Asn108His Uncertain significance ★★ ⚠ same type
POMP p.Asn40Ser Uncertain significance ★★ ⚠ same type
POMP p.Gln56His 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/pomp-p-pro76thr (accessed [today's date]).

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