Is CD177 p.Thr210Ile (c.629C>T) pathogenic?

CD177 p.Thr210Ile (c.629C>T) is classified Benign/Likely benign in CD177 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-01-01). Rare (popmax 0.957%, mid).

How common is CD177 p.Thr210Ile (c.629C>T) in the general population?

CD177 p.Thr210Ile (c.629C>T) is rare (popmax 0.957%, mid) (gnomAD).

CD177 p.Thr210Ile

c.629C>T · rs182368720 · VCV777054

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.957%, mid)

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 -5.5	GERP -2.3
Regional constraint	o/e 1.18	unconstrained · MANE · 8,602 bp · p 3.2e-05 · regional, not allelic
Overall
CADD	0.079	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.957% Middle Eastern · 58/6,060 alleles

Filtering AF 0.76% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.689%

Overall 0.418% 6,740/1,613,154 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.15%	87
Middle Easterngrpmax	0.957%	104
Remaining individualsnot grpmax-eligible	0.517%	193
European (non-Finnish)	0.447%	224
Finnishnot grpmax-eligible	0.419%	239
South Asian	0.316%	316
Admixed American	0.178%	560
African / African-American	0.088%	1,136
East Asian	0.0379%	2,639

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CD177
Protein: p.Thr210Ile
Coding: c.629C>T
MANE Select: NM_020406
dbSNP: rs182368720
Type: single nucleotide variant
Location: chr19:43360274 (GRCh38)
Gene constraint: LOEUF 1.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.67 · 2 PDB
Residue 210: the upar/ly6 1 domain

Full CD177 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD177 p.Gly431Arg Benign ★★ same type
CD177 p.Lys366Arg Benign ★★ same type
CD177 p.Phe208Val Benign ★★ same type
CD177 p.Ser364Thr Benign ★★ same type
CD177 p.Ala281Asp Uncertain significance ★ same type
CD177 p.Ala3Val Uncertain significance ★ same type
CD177 p.Ala425Pro Uncertain significance ★ same type
CD177 p.Arg213Gln 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/cd177-p-thr210ile (accessed [today's date]).

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