Is PITRM1 p.Ile803= (c.2409C>T) pathogenic?

PITRM1 p.Ile803= (c.2409C>T) is classified Likely benign in PITRM1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-23). Very rare (popmax 0.0068%, nfe).

How common is PITRM1 p.Ile803= (c.2409C>T) in the general population?

PITRM1 p.Ile803= (c.2409C>T) is very rare (popmax 0.0068%, nfe) (gnomAD).

PITRM1 p.Ile803=

c.2409C>T · VCV3889161

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0068%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.008	strongly benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.8	GERP -3.4
Overall
CADD	0.187	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0068% European (non-Finnish) · 78/1,146,964 alleles

Filtering AF 0.00554% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00512%

Overall 0.00548% 85/1,550,140 alleles · very rare exomes 79/1,397,868 · genomes 6/152,272 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0068%	14,705
Remaining individualsnot grpmax-eligible	0.005%	20,000
Ashkenazi Jewishnot grpmax-eligible	0.00349%	28,658
African / African-American	0.00274%	36,512
East Asian	0.00244%	40,994

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: PITRM1
Protein: p.Ile803=
Coding: c.2409C>T
MANE Select: NM_014889
Type: single nucleotide variant
Location: chr10:3145644 (GRCh38)

Full PITRM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/pitrm1-p-ile803 (accessed [today's date]).

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