Is IFT27 p.Ser72= (c.216G>A) pathogenic?

IFT27 p.Ser72= (c.216G>A) is classified Likely benign in IFT27 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-11-06). Rare (popmax 0.203%, sas).

How common is IFT27 p.Ser72= (c.216G>A) in the general population?

IFT27 p.Ser72= (c.216G>A) is rare (popmax 0.203%, sas) (gnomAD).

IFT27 p.Ser72=

c.216G>A · rs549372362 · VCV2913369

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.203%, sas)

⚠ 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
Pangolin	Δ0.30	loss · gain 0.00 · independent
Constraint at this position
Conservation	phyloP -3.7	GERP -2.8
Overall
CADD	6.067	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.203% South Asian · 185/91,078 alleles

Filtering AF 0.179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.17%

Overall 0.0122% 197/1,614,118 alleles · rare exomes 193/1,461,814 · genomes 4/152,304 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.203%	492
Middle Eastern	0.033%	3,031
Admixed American	0.00666%	15,007
Remaining individualsnot grpmax-eligible	0.0048%	20,836
European (non-Finnish)	0.000254%	393,326

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: IFT27
Protein: p.Ser72=
Coding: c.216G>A
MANE Select: NM_001177701
dbSNP: rs549372362
Type: single nucleotide variant
Location: chr22:36766156 (GRCh38)

Full IFT27 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/ift27-p-ser72 (accessed [today's date]).

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