Is MCIDAS p.Pro19= (c.57C>T) pathogenic?

MCIDAS p.Pro19= (c.57C>T) is classified Likely benign in MCIDAS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-30). Ultra-rare (popmax 0.0365%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with MCIDAS p.Pro19= (c.57C>T)?

MCIDAS p.Pro19= (c.57C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is MCIDAS p.Pro19= (c.57C>T) in the general population?

MCIDAS p.Pro19= (c.57C>T) is ultra-rare (popmax 0.0365%, amr) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

MCIDAS p.Pro19=

c.57C>T · rs1417940710 · VCV699336

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0365%, amr)

Conditions

primary ciliary dyskinesia

⚠ 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.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.6	GERP 0.45, phastCons 1
Overall
CADD	13.07	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0365% Admixed American · 18/49,332 alleles

Filtering AF 0.0235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0194%

Overall 0.00138% 21/1,516,412 alleles · ultra-rare exomes 16/1,364,288 · genomes 5/152,124 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0365%	2,741
Remaining individualsnot grpmax-eligible	0.00338%	29,571
European (non-Finnish)	8.78e-05%	1,139,203

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: MCIDAS
Protein: p.Pro19=
Coding: c.57C>T
MANE Select: NM_001190787
dbSNP: rs1417940710
Type: single nucleotide variant
Location: chr5:55227082 (GRCh38)

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

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

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/mcidas-p-pro19 (accessed [today's date]).

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