Is POMP p.Leu6Pro (c.17T>C) pathogenic?

POMP p.Leu6Pro (c.17T>C) is classified Uncertain significance in POMP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-05). AlphaMissense: likely benign (0.1059); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with POMP p.Leu6Pro (c.17T>C)?

POMP p.Leu6Pro (c.17T>C) is associated with Inborn genetic diseases (ClinVar).

How common is POMP p.Leu6Pro (c.17T>C) in the general population?

POMP p.Leu6Pro (c.17T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about POMP p.Leu6Pro (c.17T>C)?

AlphaMissense predicts likely benign (score 0.1059) — an in-silico prediction, not a clinical call.

POMP p.Leu6Pro

c.17T>C · rs1270877972 · VCV2298190

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1059 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1059	likely benign
REVEL	0.191	benign-leaning
SaProt	LLR -8.34	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 19 kb · p 0.048 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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.Leu6Pro
Coding: c.17T>C
MANE Select: NM_015932
dbSNP: rs1270877972
Type: single nucleotide variant
Location: chr13:28662423 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 81.76 · 11 PDB

Full POMP 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

POMP p.Asn108His Uncertain significance ★★ ⚠ same condition
POMP p.Asn40Ser Uncertain significance ★★ ⚠ same condition
POMP p.Gln56His Uncertain significance ★★ ⚠ same condition
POMP p.His28Pro Uncertain significance ★★ ⚠ same condition
POMP p.Ile112Val Uncertain significance ★★ ⚠ same condition
POMP p.Leu30Phe Uncertain significance ★★ ⚠ same condition
POMP p.Pro76Ser Uncertain significance ★★ ⚠ same condition
POMP p.Ser65Phe 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/pomp-p-leu6pro (accessed [today's date]).

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