Is USH2A p.Ser2170= (c.6510T>C) pathogenic?

USH2A p.Ser2170= (c.6510T>C) is classified Likely benign in USH2A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-26). No allele count reported in gnomAD v4.1 (AN 1,612,508).

How common is USH2A p.Ser2170= (c.6510T>C) in the general population?

USH2A p.Ser2170= (c.6510T>C) is no allele count reported in gnomAD v4.1 (AN 1,612,508) (gnomAD).

USH2A p.Ser2170=

c.6510T>C · rs373604102 · VCV2414065

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,508)

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 0.2	GERP -4.3, phastCons 0.17
Overall
CADD	1.547	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,612,508). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: USH2A
Protein: p.Ser2170=
Coding: c.6510T>C
MANE Select: NM_206933
dbSNP: rs373604102
Type: single nucleotide variant
Location: chr1:215999034 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2170: the fibronectin type-iii 8 domain

Full USH2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

USH2A p.Ser2170Arg Benign/Likely benign ★★ same residue
USH2A p.Ser2170Cys Uncertain significance ★ ⚠ same residue
USH2A p.Ser2170Ile Uncertain significance ★ ⚠ same residue
USH2A p.Ser2170Asn Likely benign ★ same residue
USH2A c.12295-3T>A Pathogenic ★★★ same type
USH2A c.8559-2A>G Pathogenic ★★★ same type
USH2A c.8682-9A>G Pathogenic ★★★ same type
USH2A p.Ala4740Asp Pathogenic ★★★ ⚠ 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/ush2a-p-ser2170 (accessed [today's date]).

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