Is CD6 p.Ser625= (c.1875C>G) pathogenic?

CD6 p.Ser625= (c.1875C>G) is classified Benign in CD6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-26). Rare (popmax 0.709%, afr); Associated with CD6-related disorder.

What condition is associated with CD6 p.Ser625= (c.1875C>G)?

CD6 p.Ser625= (c.1875C>G) is associated with CD6-related disorder (ClinVar).

How common is CD6 p.Ser625= (c.1875C>G) in the general population?

CD6 p.Ser625= (c.1875C>G) is rare (popmax 0.709%, afr) (gnomAD).

CD6 p.Ser625=

c.1875C>G · rs111507268 · VCV3038860

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.709%, afr)

Conditions

CD6-related disorder

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 -14	GERP -3.1
Overall
CADD	0.501	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.709% African / African-American · 531/74,944 alleles

Filtering AF 0.659% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.639%

Overall 0.0365% 587/1,608,282 alleles · rare exomes 299/1,456,010 · genomes 288/152,272 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.709%	141
Admixed American	0.0471%	2,124
Remaining individualsnot grpmax-eligible	0.0402%	2,488
Middle Eastern	0.0171%	5,832
European (non-Finnish)	0.00017%	588,789

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: CD6
Protein: p.Ser625=
Coding: c.1875C>G
MANE Select: NM_006725
dbSNP: rs111507268
Type: single nucleotide variant
Location: chr11:61018326 (GRCh38)
Gene constraint: LOEUF 1.03 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.14 · 1 PDB
Residue 625: the 'disordered' region

Full CD6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD6-related disorder

Similar variants

CD6 c.49+8C>T Benign same condition
CD6 p.Ala257= Benign same condition
CD6 p.Ala257Val Benign same condition
CD6 p.Ala271Thr Benign same condition
CD6 p.Ala605= Benign same condition
CD6 p.Arg225Trp Benign same condition
CD6 p.Gly606Ser Benign same condition
CD6 p.Pro433= Likely benign same condition

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/cd6-p-ser625 (accessed [today's date]).

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