Is MTPAP p.Pro393= (c.1179C>A) pathogenic?

MTPAP p.Pro393= (c.1179C>A) is classified Likely benign in MTPAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-18). Very rare (popmax 0.00891%, eas).

How common is MTPAP p.Pro393= (c.1179C>A) in the general population?

MTPAP p.Pro393= (c.1179C>A) is very rare (popmax 0.00891%, eas) (gnomAD).

MTPAP p.Pro393=

c.1179C>A · rs764694615 · VCV3005352

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.6	GERP -3.9
Overall
CADD	3.768	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00891% East Asian · 4/44,880 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.000248% 4/1,613,172 alleles · very rare exomes 4/1,460,938 · genomes 0/152,234 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MTPAP
Protein: p.Pro393=
Coding: c.1179C>A
MANE Select: NM_018109
dbSNP: rs764694615
Type: single nucleotide variant
Location: chr10:30322431 (GRCh38)
Gene constraint: LOEUF 0.641 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 83.16 · 1 PDB

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

Similar variants

MTPAP p.Pro393Leu Uncertain significance ★ ⚠ same residue
MTPAP p.Pro393Ser Uncertain significance ★ ⚠ same residue
MTPAP p.Asn478Asp Pathogenic ★★ ⚠ same type
MTPAP p.Ala141Thr Uncertain significance ★★ ⚠ same type
MTPAP p.Ala219Thr Uncertain significance ★★ ⚠ same type
MTPAP p.Arg160Trp Uncertain significance ★★ ⚠ same type
MTPAP p.Arg171Cys Uncertain significance ★★ ⚠ same type
MTPAP p.Arg461Gln 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/mtpap-p-pro393 (accessed [today's date]).

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