Is BTBD17 p.Pro210= (c.630C>T) pathogenic?

BTBD17 p.Pro210= (c.630C>T) is classified Likely benign in BTBD17 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-01). Ultra-rare (popmax 0.017%, nfe).

How common is BTBD17 p.Pro210= (c.630C>T) in the general population?

BTBD17 p.Pro210= (c.630C>T) is ultra-rare (popmax 0.017%, nfe) (gnomAD).

BTBD17 p.Pro210=

c.630C>T · rs922141420 · VCV3250687

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.017%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.4	GERP -2.2
Overall
CADD	1.761	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.017% European (non-Finnish) · 199/1,170,484 alleles

Filtering AF 0.0151% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.0129% 204/1,577,274 alleles · ultra-rare exomes 194/1,425,128 · genomes 10/152,146 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.017%	5,882
Remaining individualsnot grpmax-eligible	0.00489%	20,461
African / African-American	0.0027%	37,041

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: BTBD17
Protein: p.Pro210=
Coding: c.630C>T
MANE Select: NM_001080466
dbSNP: rs922141420
Type: single nucleotide variant
Location: chr17:74357464 (GRCh38)
Gene constraint: LOEUF 1.489 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.20
Residue 210: the back domain

Full BTBD17 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BTBD17 p.Ala113Thr Uncertain significance ★ ⚠ same type
BTBD17 p.Ala160Val Uncertain significance ★ ⚠ same type
BTBD17 p.Ala248Thr Uncertain significance ★ ⚠ same type
BTBD17 p.Ala254Val Uncertain significance ★ ⚠ same type
BTBD17 p.Ala301Val Uncertain significance ★ ⚠ same type
BTBD17 p.Ala310Thr Uncertain significance ★ ⚠ same type
BTBD17 p.Ala350Glu Uncertain significance ★ ⚠ same type
BTBD17 p.Ala350Ser 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/btbd17-p-pro210 (accessed [today's date]).

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